diff --git a/biolink-model.yaml b/biolink-model.yaml index ec8d6ae48..854cc910a 100644 --- a/biolink-model.yaml +++ b/biolink-model.yaml @@ -8213,7 +8213,7 @@ classes: - NCIT - SNOMEDCT - medgen - - ICD11 + - icd11 - icd11.foundation - ICD10 - ICD9 diff --git a/project/jsonld/biolink_model.context.jsonld b/project/jsonld/biolink_model.context.jsonld index aaf5d7b15..4d9216008 100644 --- a/project/jsonld/biolink_model.context.jsonld +++ b/project/jsonld/biolink_model.context.jsonld @@ -1,7 +1,7 @@ { "comments": { "description": "Auto generated by LinkML jsonld context generator", - "generation_date": "2025-01-09T18:18:14", + "generation_date": "2025-01-10T08:43:20", "source": "biolink_model.yaml" }, "@context": { @@ -230,7 +230,6 @@ "@prefix": true }, "ICD10": "https://icd.who.int/browse10/2016/en#/", - "ICD11": "http://id.who.int/icd/entity/", "ICD9": { "@id": "http://translator.ncats.nih.gov/ICD9_", "@prefix": true diff --git a/project/jsonld/biolink_model.jsonld b/project/jsonld/biolink_model.jsonld index 25ac1b309..a3a10b25a 100644 --- a/project/jsonld/biolink_model.jsonld +++ b/project/jsonld/biolink_model.jsonld @@ -27232,7 +27232,7 @@ "NCIT", "SNOMEDCT", "medgen", - "ICD11", + "icd11", "icd11.foundation", "ICD10", "ICD9", @@ -35901,9 +35901,9 @@ ], "metamodel_version": "1.7.0", "source_file": "biolink_model.yaml", - "source_file_date": "2025-01-09T18:18:11", + "source_file_date": "2025-01-10T08:43:16", "source_file_size": 404136, - "generation_date": "2025-01-09T18:18:17", + "generation_date": "2025-01-10T08:43:22", "@type": "SchemaDefinition", "@context": [ "project/jsonld/biolink_model.context.jsonld", diff --git a/project/owl/biolink_model.owl.ttl b/project/owl/biolink_model.owl.ttl index 1b3436061..51206e6ee 100644 --- a/project/owl/biolink_model.owl.ttl +++ b/project/owl/biolink_model.owl.ttl @@ -2599,13 +2599,13 @@ biolink:AccessibleDnaRegion a owl:Class ; rdfs:label "accessible dna region" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], @@ -2654,29 +2654,29 @@ biolink:AccessibleDnaRegion a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity ontogenic association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], @@ -2687,31 +2687,31 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a owl:Class ; biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a owl:Class ; rdfs:label "anatomical entity to anatomical entity part of association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], biolink:AnatomicalEntityToAnatomicalEntityAssociation ; skos:definition "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; @@ -2803,26 +2803,26 @@ biolink:Bacterium a owl:Class ; biolink:BehaviorToBehavioralFeatureAssociation a owl:Class ; rdfs:label "behavior to behavioral feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:BehavioralFeature ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Behavior ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Behavior ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:BehavioralFeature ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; skos:inScheme . @@ -2850,20 +2850,20 @@ biolink:BioticExposure a owl:Class ; biolink:Book a owl:Class ; rdfs:label "book" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], biolink:Publication ; skos:definition "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; skos:inScheme . @@ -2889,29 +2889,29 @@ biolink:CaseToPhenotypicFeatureAssociation a owl:Class ; biolink:CausalGeneToDiseaseAssociation a owl:Class ; rdfs:label "causal gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -3004,19 +3004,19 @@ biolink:Cell a owl:Class ; biolink:CellLineAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "cell line as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:CellLine ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; skos:inScheme . @@ -3030,184 +3030,181 @@ biolink:CellLineToEntityAssociationMixin a owl:Class ; biolink:ChemicalAffectsGeneAssociation a owl:Class ; rdfs:label "chemical affects gene association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; + owl:minCardinality 0 ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:species_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - biolink:Association ; + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], + biolink:Association ; skos:definition "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; skos:inScheme . biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; rdfs:label "chemical entity assesses named thing association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; @@ -3215,56 +3212,59 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; rdfs:label "chemical entity or gene or gene product regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], biolink:Association ; skos:definition "A regulatory relationship between two genes" ; skos:inScheme . @@ -3272,107 +3272,107 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a owl:Class ; biolink:ChemicalGeneInteractionAssociation a owl:Class ; rdfs:label "chemical gene interaction association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:object_form_or_variant_qualifier ], biolink:Association ; skos:definition "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; skos:exactMatch SIO:001257 ; @@ -3381,19 +3381,19 @@ biolink:ChemicalGeneInteractionAssociation a owl:Class ; biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment side effect disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; @@ -3424,36 +3424,36 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:MacromolecularMachineMixin ; owl:onProperty biolink:catalyst_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:catalyst_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:catalyst_qualifier ], biolink:ChemicalToChemicalAssociation ; skos:definition "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; skos:inScheme . @@ -3461,20 +3461,20 @@ biolink:ChemicalToChemicalDerivationAssociation a owl:Class ; biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], biolink:Association ; skos:definition "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; skos:inScheme ; @@ -3483,14 +3483,14 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; biolink:ChemicalToPathwayAssociation a owl:Class ; rdfs:label "chemical to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], @@ -3498,8 +3498,8 @@ biolink:ChemicalToPathwayAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -3549,13 +3549,13 @@ biolink:ClinicalFinding a owl:Class ; biolink:ClinicalMeasurement a owl:Class ; rdfs:label "clinical measurement" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:has_attribute_type ], biolink:ClinicalAttribute ; skos:definition "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; @@ -3618,38 +3618,38 @@ biolink:ConfidenceLevel a owl:Class ; biolink:ContributorAssociation a owl:Class ; rdfs:label "contributor association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:InformationContentEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualifiers ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:InformationContentEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Agent ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:qualifiers ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:qualifiers ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualifiers ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; skos:inScheme . @@ -3657,29 +3657,29 @@ biolink:ContributorAssociation a owl:Class ; biolink:CorrelatedGeneToDiseaseAssociation a owl:Class ; rdfs:label "correlated gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -3708,26 +3708,26 @@ biolink:DiseaseOrPhenotypicFeatureExposure a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to genetic inheritance association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneticInheritance ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneticInheritance ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; skos:inScheme . @@ -3735,16 +3735,16 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a owl:Class ; biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a owl:Class ; rdfs:label "disease or phenotypic feature to location association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], - [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; @@ -3765,41 +3765,41 @@ biolink:DiseaseToExposureEventAssociation a owl:Class ; biolink:DiseaseToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "disease to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:onset_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Onset ; - owl:onProperty biolink:onset_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:PhenotypicFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:FrequencyQuantifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:Onset ; owl:onProperty biolink:onset_qualifier ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin ], biolink:Association ; skos:closeMatch dcid:DiseaseSymptomAssociation ; skos:definition "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; @@ -3851,16 +3851,16 @@ biolink:DrugToEntityAssociationMixin a owl:Class ; biolink:DrugToGeneAssociation a owl:Class ; rdfs:label "drug to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:DrugToEntityAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a drug and a gene or gene product." ; @@ -3899,58 +3899,58 @@ biolink:DrugToGeneInteractionExposure a owl:Class ; biolink:DruggableGeneToDiseaseAssociation a owl:Class ; rdfs:label "druggable gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:DruggableGeneCategoryEnum ; owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], biolink:GeneToDiseaseAssociation ; skos:inScheme . biolink:EntityToDiseaseAssociation a owl:Class ; rdfs:label "entity to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ResearchPhaseEnum ; owl:onProperty biolink:max_research_phase ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; - owl:onProperty biolink:clinical_approval_status ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_approval_status ], + owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:clinical_approval_status ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ResearchPhaseEnum ; - owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:max_research_phase ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:clinical_approval_status ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ClinicalApprovalStatusEnum ; + owl:onProperty biolink:clinical_approval_status ], biolink:Association ; skos:inScheme . @@ -3969,12 +3969,6 @@ biolink:EntityToOutcomeAssociationMixin a owl:Class ; biolink:EntityToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "entity to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:max_research_phase ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:clinical_approval_status ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; @@ -3983,9 +3977,15 @@ biolink:EntityToPhenotypicFeatureAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:clinical_approval_status ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:max_research_phase ], [ a owl:Restriction ; owl:allValuesFrom biolink:ResearchPhaseEnum ; owl:onProperty biolink:max_research_phase ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:clinical_approval_status ], biolink:Association ; skos:inScheme . @@ -4026,19 +4026,19 @@ biolink:Event a owl:Class ; biolink:ExonToTranscriptRelationship a owl:Class ; rdfs:label "exon to transcript relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Exon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Transcript ; @@ -4050,11 +4050,14 @@ biolink:ExonToTranscriptRelationship a owl:Class ; biolink:ExposureEventToOutcomeAssociation a owl:Class ; rdfs:label "exposure event to outcome association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:population_context_qualifier ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:temporal_context_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:population_context_qualifier ], @@ -4064,9 +4067,6 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:temporal_context_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:temporal_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:time ; owl:onProperty biolink:temporal_context_qualifier ], @@ -4077,11 +4077,11 @@ biolink:ExposureEventToOutcomeAssociation a owl:Class ; biolink:ExposureEventToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "exposure event to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ExposureEvent ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -4144,176 +4144,176 @@ biolink:Fungus a owl:Class ; biolink:GeneAffectsChemicalAssociation a owl:Class ; rdfs:label "gene affects chemical association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_derivative_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:object_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; owl:onProperty biolink:object_part_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalPartQualifierEnum ; - owl:onProperty biolink:subject_part_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:anatomical_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityDerivativeEnum ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalOrGeneOrGeneProductFormOrVariantEnum ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:subject_direction_qualifier ], biolink:Association ; skos:definition "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; skos:inScheme . @@ -4321,17 +4321,17 @@ biolink:GeneAffectsChemicalAssociation a owl:Class ; biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "gene as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], @@ -4341,41 +4341,41 @@ biolink:GeneAsAModelOfDiseaseAssociation a owl:Class ; biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; rdfs:label "gene has variant that contributes to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], biolink:GeneToDiseaseAssociation ; skos:inScheme . @@ -4667,68 +4667,68 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a owl:Class ; biolink:GeneRegulatesGeneAssociation a owl:Class ; rdfs:label "gene regulates gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:minCardinality 0 ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Describes a regulatory relationship between two genes or gene products." ; skos:inScheme . @@ -4737,26 +4737,17 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; rdfs:label "gene to expression site association" ; rdfs:seeAlso ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:stage_qualifier ], + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; owl:onProperty biolink:object ], @@ -4764,23 +4755,32 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:stage_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:stage_qualifier ], biolink:Association ; skos:definition "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; skos:editorialNote "TBD: introduce subclasses for distinction between wild-type and experimental conditions?" ; @@ -4789,16 +4789,16 @@ biolink:GeneToExpressionSiteAssociation a owl:Class ; biolink:GeneToGeneCoexpressionAssociation a owl:Class ; rdfs:label "gene to gene coexpression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneExpressionMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], biolink:GeneToGeneAssociation ; skos:definition "Indicates that two genes are co-expressed, generally under the same conditions." ; @@ -4807,23 +4807,23 @@ biolink:GeneToGeneCoexpressionAssociation a owl:Class ; biolink:GeneToGeneFamilyAssociation a owl:Class ; rdfs:label "gene to gene family association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneFamily ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneFamily ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], @@ -4832,7 +4832,7 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; skos:inScheme . @@ -4840,32 +4840,32 @@ biolink:GeneToGeneFamilyAssociation a owl:Class ; biolink:GeneToGeneHomologyAssociation a owl:Class ; rdfs:label "gene to gene homology association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], biolink:GeneToGeneAssociation ; skos:definition "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; skos:inScheme . @@ -4873,32 +4873,32 @@ biolink:GeneToGeneHomologyAssociation a owl:Class ; biolink:GeneToGeneProductRelationship a owl:Class ; rdfs:label "gene to gene product relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneProductMixin ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:GeneProductMixin ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is transcribed and potentially translated to a gene product" ; skos:inScheme . @@ -4907,22 +4907,22 @@ biolink:GeneToGoTermAssociation a owl:Class ; rdfs:label "gene to go term association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:subject ], biolink:FunctionalAssociation ; skos:altLabel "functional association" ; skos:exactMatch WBVocab:Gene-GO-Association ; @@ -4932,25 +4932,25 @@ biolink:GeneToPathwayAssociation a owl:Class ; rdfs:label "gene to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An interaction between a gene or gene product and a biological process or pathway." ; skos:inScheme . @@ -4958,29 +4958,29 @@ biolink:GeneToPathwayAssociation a owl:Class ; biolink:GeneToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:PhenotypicFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; skos:exactMatch WBVocab:Gene-Phenotype-Association ; skos:inScheme . @@ -4992,10 +4992,10 @@ biolink:Genome a owl:Class ; owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:GenomicEntity ], biolink:BiologicalEntity ; skos:closeMatch dcid:GenomeAssemblyUnit ; skos:definition "A genome is the sum of genetic material within a cell or virion." ; @@ -5007,23 +5007,23 @@ biolink:Genome a owl:Class ; biolink:GenomicBackgroundExposure a owl:Class ; rdfs:label "genomic background exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent ], + owl:someValuesFrom biolink:ThingWithTaxon ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon ], + owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneGroupingMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], biolink:Attribute ; skos:definition "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; skos:inScheme . @@ -5031,14 +5031,14 @@ biolink:GenomicBackgroundExposure a owl:Class ; biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "genotype as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], @@ -5051,32 +5051,32 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a owl:Class ; biolink:GenotypeToGeneAssociation a owl:Class ; rdfs:label "genotype to gene association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], biolink:Association ; skos:definition "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; skos:inScheme . @@ -5086,30 +5086,30 @@ biolink:GenotypeToGenotypePartAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Genotype ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Any association between one genotype and a genotypic entity that is a sub-component of it" ; skos:inScheme . @@ -5118,28 +5118,28 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "genotype to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; skos:inScheme . @@ -5147,32 +5147,32 @@ biolink:GenotypeToPhenotypicFeatureAssociation a owl:Class ; biolink:GenotypeToVariantAssociation a owl:Class ; rdfs:label "genotype to variant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Any association between a genotype and a sequence variant." ; skos:inScheme . @@ -5278,30 +5278,30 @@ biolink:InformationContentEntityToNamedThingAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; skos:inScheme . @@ -5380,14 +5380,14 @@ biolink:MacromolecularComplex a owl:Class ; biolink:MacromolecularMachineToBiologicalProcessAssociation a owl:Class ; rdfs:label "macromolecular machine to biological process association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:object ], @@ -5400,15 +5400,15 @@ biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:CellularComponent ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CellularComponent ; - owl:onProperty biolink:object ], biolink:FunctionalAssociation ; skos:definition "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; skos:inScheme . @@ -5416,14 +5416,14 @@ biolink:MacromolecularMachineToCellularComponentAssociation a owl:Class ; biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; rdfs:label "macromolecular machine to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], - [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], @@ -5434,32 +5434,32 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a owl:Class ; biolink:MaterialSampleDerivationAssociation a owl:Class ; rdfs:label "material sample derivation association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:MaterialSample ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a material sample and the material entity from which it is derived." ; skos:inScheme . @@ -5468,10 +5468,10 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "material sample to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:definition "An association between a material sample and a disease or phenotype." ; skos:inScheme . @@ -5493,23 +5493,23 @@ biolink:MicroRNA a owl:Class ; biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; rdfs:label "molecular activity to chemical entity association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:ChemicalEntity ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; skos:inScheme . @@ -5517,22 +5517,22 @@ biolink:MolecularActivityToChemicalEntityAssociation a owl:Class ; biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; rdfs:label "molecular activity to molecular activity association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:MolecularActivity ; owl:onProperty biolink:object ], biolink:Association ; skos:definition "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; @@ -5541,31 +5541,31 @@ biolink:MolecularActivityToMolecularActivityAssociation a owl:Class ; biolink:MolecularActivityToPathwayAssociation a owl:Class ; rdfs:label "molecular activity to pathway association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Pathway ; - owl:onProperty biolink:object ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularActivity ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:Pathway ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:allValuesFrom biolink:MolecularActivity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Association that holds the relationship between a reaction and the pathway it participates in." ; @@ -5575,76 +5575,76 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a owl:Class ; rdfs:label "named thing associated with likelihood of named thing association" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_context_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 0 ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:population_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:population_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_context_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:population_context_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:population_context_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], biolink:Association ; skos:inScheme . @@ -5659,10 +5659,10 @@ biolink:NucleosomeModification a owl:Class ; rdfs:label "nucleosome modification" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductIsoformMixin ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:GeneProductIsoformMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EpigenomicEntity ], @@ -5679,76 +5679,76 @@ biolink:ObservedExpectedFrequencyAnalysisResult a owl:Class ; biolink:OrganismTaxonToEnvironmentAssociation a owl:Class ; rdfs:label "organism taxon to environment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], biolink:Association ; skos:inScheme . biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; rdfs:label "organism taxon to organism taxon interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:associated_environmental_context ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:associated_environmental_context ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; skos:inScheme . @@ -5756,13 +5756,10 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a owl:Class ; biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; rdfs:label "organism taxon to organism taxon specialization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; @@ -5771,16 +5768,19 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a owl:Class ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], biolink:OrganismTaxonToOrganismTaxonAssociation ; skos:definition "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; @@ -5793,74 +5793,77 @@ biolink:OrganismToOrganismAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:IndividualOrganism ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . biolink:OrganismalEntityAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "organismal entity as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:OrganismalEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismalEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], biolink:Association ; skos:inScheme . biolink:PairwiseMolecularInteraction a owl:Class ; rdfs:label "pairwise molecular interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:interacting_molecules_category ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:MolecularEntity ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:interacting_molecules_category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], @@ -5869,13 +5872,10 @@ biolink:PairwiseMolecularInteraction a owl:Class ; owl:onProperty biolink:interacting_molecules_category ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:interacting_molecules_category ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], biolink:PairwiseGeneToGeneInteraction ; skos:definition "An interaction at the molecular level between two physical entities" ; skos:inScheme . @@ -5967,20 +5967,20 @@ biolink:Phenomenon a owl:Class ; biolink:PhenotypicFeatureToDiseaseAssociation a owl:Class ; rdfs:label "phenotypic feature to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme . @@ -5988,10 +5988,10 @@ biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "phenotypic feature to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], biolink:Association ; skos:definition "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ; skos:inScheme . @@ -6038,31 +6038,31 @@ biolink:Plant a owl:Class ; biolink:PopulationToPopulationAssociation a owl:Class ; rdfs:label "population to population association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a two populations" ; @@ -6080,194 +6080,194 @@ biolink:PosttranslationalModification a owl:Class ; biolink:PredicateMapping a owl:Class ; rdfs:label "predicate mapping" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:broad_match ], - [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_derivative_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:narrow_match ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:mapped_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_part_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_derivative_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_derivative_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_part_qualifier ], + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject_part_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_context_qualifier ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:narrow_match ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:subject_context_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_derivative_qualifier ], + owl:onProperty biolink:subject_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_context_qualifier ], + owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:mapped_predicate ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:causal_mechanism_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:exact_match ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:broad_match ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_derivative_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_part_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:narrow_match ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_context_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CausalMechanismQualifierEnum ; owl:onProperty biolink:causal_mechanism_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_derivative_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; - owl:onProperty biolink:broad_match ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_derivative_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:narrow_match ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_form_or_variant_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_form_or_variant_qualifier ], + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:object_part_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object_form_or_variant_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:broad_match ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:exact_match ], + owl:onProperty biolink:subject_derivative_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_part_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_form_or_variant_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], linkml:ClassDefinition ; skos:definition "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; skos:inScheme . @@ -6283,32 +6283,32 @@ biolink:PreprintPublication a owl:Class ; biolink:ProcessRegulatesProcessAssociation a owl:Class ; rdfs:label "process regulates process association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:BiologicalProcess ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalProcess ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "Describes a regulatory relationship between two genes or gene products." ; skos:inScheme . @@ -6324,10 +6324,10 @@ biolink:ProteinDomain a owl:Class ; rdfs:label "protein domain" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GeneGroupingMixin ], biolink:BiologicalEntity ; skos:definition "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; skos:exactMatch , @@ -6339,10 +6339,10 @@ biolink:ProteinFamily a owl:Class ; rdfs:label "protein family" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GeneGroupingMixin ], biolink:BiologicalEntity ; skos:exactMatch , WIKIDATA:Q2278983 ; @@ -6403,10 +6403,10 @@ biolink:RNAProductIsoform a owl:Class ; biolink:ReactionToCatalystAssociation a owl:Class ; rdfs:label "reaction to catalyst association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -6421,10 +6421,10 @@ biolink:ReagentTargetedGene a owl:Class ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], biolink:BiologicalEntity ; skos:altLabel "sequence targeting reagent" ; skos:definition "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; @@ -6501,23 +6501,23 @@ biolink:SequenceEnum a owl:Class ; biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; rdfs:label "sequence variant modulates treatment association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Treatment ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Treatment ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; skos:inScheme ; @@ -6526,44 +6526,44 @@ biolink:SequenceVariantModulatesTreatmentAssociation a owl:Class ; biolink:Serial a owl:Class ; rdfs:label "serial" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], + owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:issue ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], @@ -6615,14 +6615,14 @@ biolink:Snv a owl:Class ; biolink:SocioeconomicExposure a owl:Class ; rdfs:label "socioeconomic exposure" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:SocioeconomicAttribute ; - owl:onProperty biolink:has_attribute ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:has_attribute ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:SocioeconomicAttribute ; + owl:onProperty biolink:has_attribute ], biolink:Attribute ; skos:definition "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; skos:inScheme . @@ -6664,23 +6664,23 @@ biolink:StudyVariable a owl:Class ; biolink:TaxonToTaxonAssociation a owl:Class ; rdfs:label "taxon to taxon association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:inScheme . @@ -6700,23 +6700,23 @@ biolink:TextMiningResult a owl:Class ; biolink:TranscriptToGeneRelationship a owl:Class ; rdfs:label "transcript to gene relationship" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:Transcript ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:SequenceFeatureRelationship ; skos:definition "A gene is a collection of transcripts" ; skos:inScheme . @@ -6725,16 +6725,16 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; rdfs:label "transcription factor binding site" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], biolink:RegulatoryRegion ; skos:altLabel "binding site", "tf binding site" ; @@ -6745,36 +6745,36 @@ biolink:TranscriptionFactorBindingSite a owl:Class ; biolink:VariantAsAModelOfDiseaseAssociation a owl:Class ; rdfs:label "variant as a model of disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], biolink:VariantToDiseaseAssociation ; skos:inScheme . biolink:VariantToGeneExpressionAssociation a owl:Class ; rdfs:label "variant to gene expression association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneExpressionMixin ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], biolink:VariantToGeneAssociation ; skos:definition "An association between a variant and expression of a gene (i.e. e-QTL)" ; @@ -6784,78 +6784,78 @@ biolink:VariantToPhenotypicFeatureAssociation a owl:Class ; rdfs:label "variant to phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme . biolink:VariantToPopulationAssociation a owl:Class ; rdfs:label "variant to population association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:FrequencyQualifierMixin ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_quotient ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_quotient ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_count ], + owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_count ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_total ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + owl:someValuesFrom biolink:FrequencyQuantifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_count ], [ a owl:Restriction ; owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PopulationOfIndividualOrganisms ; - owl:onProperty biolink:object ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:has_quotient ], biolink:Association ; skos:definition "An association between a variant and a population, where the variant has particular frequency in the population" ; skos:inScheme . @@ -7421,40 +7421,40 @@ biolink:Article a owl:Class ; rdfs:label "article" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:iso_abbreviation ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:issue ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:maxCardinality 1 ; owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:iso_abbreviation ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:published_in ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:volume ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:iso_abbreviation ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:issue ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:volume ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:iso_abbreviation ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:published_in ], biolink:Publication ; skos:definition "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; skos:exactMatch fabio:article, @@ -7487,32 +7487,32 @@ biolink:BehavioralFeature a owl:Class ; biolink:BookChapter a owl:Class ; rdfs:label "book chapter" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:published_in ], - [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:chapter ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:chapter ], + owl:onProperty biolink:published_in ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:volume ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:published_in ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:chapter ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:published_in ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:published_in ], + owl:onProperty biolink:volume ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:volume ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:volume ], + owl:minCardinality 0 ; + owl:onProperty biolink:chapter ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:published_in ], biolink:Publication ; skos:inScheme . @@ -7532,18 +7532,18 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:CellLineToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; skos:inScheme . @@ -7563,14 +7563,14 @@ biolink:ChemicalEntityToEntityAssociationMixin a owl:Class ; biolink:ChemicalExposure a owl:Class ; rdfs:label "chemical exposure" ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:QuantityValue ; + owl:onProperty biolink:has_quantitative_value ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_quantitative_value ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:QuantityValue ; - owl:onProperty biolink:has_quantitative_value ], biolink:Attribute ; skos:definition "A chemical exposure is an intake of a particular chemical entity." ; skos:exactMatch ECTO:9000000, @@ -7580,32 +7580,32 @@ biolink:ChemicalExposure a owl:Class ; biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "chemical or drug or treatment to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; owl:onProperty biolink:FDA_adverse_event_level ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin ], + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; - owl:allValuesFrom biolink:FDAIDAAdverseEventEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:FDA_adverse_event_level ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:FDA_adverse_event_level ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is a secondary undesirable effect." ; skos:inScheme . @@ -7716,10 +7716,10 @@ biolink:GeneFamily a owl:Class ; rdfs:label "gene family" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GeneGroupingMixin ], biolink:BiologicalEntity ; skos:altLabel "orthogroup", "protein family" ; @@ -7734,74 +7734,74 @@ biolink:GeneFamily a owl:Class ; biolink:GenomicSequenceLocalization a owl:Class ; rdfs:label "genomic sequence localization" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:phase ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:start_interbase_coordinate ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:genome_build ], + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:strand ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:start_interbase_coordinate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:end_interbase_coordinate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:StrandEnum ; - owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:end_interbase_coordinate ], + owl:onProperty biolink:strand ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:strand ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:StrandEnum ; - owl:onProperty biolink:genome_build ], + owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:strand ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:phase ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:genome_build ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhaseEnum ; + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:start_interbase_coordinate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:StrandEnum ; + owl:onProperty biolink:strand ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:start_interbase_coordinate ], + owl:onProperty biolink:phase ], [ a owl:Restriction ; owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:end_interbase_coordinate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhaseEnum ; - owl:onProperty biolink:phase ], + owl:maxCardinality 1 ; + owl:onProperty biolink:start_interbase_coordinate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:end_interbase_coordinate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:StrandEnum ; + owl:onProperty biolink:genome_build ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:genome_build ], @@ -7816,17 +7816,20 @@ biolink:GenotypeToDiseaseAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; @@ -7836,16 +7839,13 @@ biolink:GenotypeToDiseaseAssociation a owl:Class ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -7860,9 +7860,6 @@ biolink:GeographicLocation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:latitude ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:latitude ], [ a owl:Restriction ; owl:allValuesFrom xsd:float ; owl:onProperty biolink:latitude ], @@ -7872,6 +7869,9 @@ biolink:GeographicLocation a owl:Class ; [ a owl:Restriction ; owl:allValuesFrom xsd:float ; owl:onProperty biolink:longitude ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:latitude ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:longitude ], @@ -7916,10 +7916,10 @@ biolink:OrganismTaxonToEntityAssociation a owl:Class ; biolink:PairwiseGeneToGeneInteraction a owl:Class ; rdfs:label "pairwise gene to gene interaction" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; @@ -7941,10 +7941,10 @@ biolink:Polypeptide a owl:Class ; rdfs:label "polypeptide" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], biolink:BiologicalEntity ; skos:altLabel "amino acid entity" ; skos:definition "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; @@ -7956,41 +7956,41 @@ biolink:Polypeptide a owl:Class ; biolink:ReactionToParticipantAssociation a owl:Class ; rdfs:label "reaction to participant association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:ReactionDirectionEnum ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:reaction_side ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:reaction_side ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:stoichiometry ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ReactionSideEnum ; + owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:reaction_side ], [ a owl:Restriction ; owl:allValuesFrom xsd:integer ; owl:onProperty biolink:stoichiometry ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ReactionSideEnum ; - owl:onProperty biolink:reaction_side ], + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ReactionDirectionEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:reaction_direction ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:stoichiometry ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:reaction_direction ], biolink:ChemicalToChemicalAssociation ; skos:inScheme . @@ -8022,26 +8022,26 @@ biolink:StudyPopulation a owl:Class ; biolink:Treatment a owl:Class ; rdfs:label "treatment" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Device ; - owl:onProperty biolink:has_device ], - [ a owl:Restriction ; owl:allValuesFrom biolink:Procedure ; owl:onProperty biolink:has_procedure ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_procedure ], + owl:allValuesFrom biolink:Device ; + owl:onProperty biolink:has_device ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_drug ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Drug ; - owl:onProperty biolink:has_drug ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ExposureEvent ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_procedure ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Drug ; + owl:onProperty biolink:has_drug ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_device ], @@ -8057,38 +8057,38 @@ biolink:Treatment a owl:Class ; biolink:VariantToDiseaseAssociation a owl:Class ; rdfs:label "variant to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom owl:Thing ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom owl:Thing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom owl:Thing ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], biolink:Association ; skos:inScheme ; skos:note "TODO decide no how to model pathogenicity" . @@ -8096,23 +8096,23 @@ biolink:VariantToDiseaseAssociation a owl:Class ; biolink:VariantToGeneAssociation a owl:Class ; rdfs:label "variant to gene association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], - [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:Gene ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:VariantToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], @@ -8798,19 +8798,19 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a owl:Class ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], biolink:Association ; skos:inScheme . @@ -8842,14 +8842,8 @@ biolink:ChemicalRole a owl:Class ; biolink:ChemicalToChemicalAssociation a owl:Class ; rdfs:label "chemical to chemical association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:ChemicalEntity ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], @@ -8857,20 +8851,26 @@ biolink:ChemicalToChemicalAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntity ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], biolink:Association ; skos:definition "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; skos:inScheme . @@ -8958,56 +8958,56 @@ biolink:FrequencyQualifierMixin a owl:Class ; biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a owl:Class ; rdfs:label "gene to disease or phenotypic feature association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProductOrChemicalEntityAspectEnum ; owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], biolink:Association ; skos:inScheme ; skos:narrowMatch WBVocab:Gene-Phenotype-Association, @@ -9065,24 +9065,24 @@ biolink:OrganismTaxonToOrganismTaxonAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], [ a owl:Restriction ; owl:allValuesFrom biolink:OrganismTaxon ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], biolink:Association ; skos:definition "A relationship between two organism taxon nodes" ; skos:inScheme . @@ -9130,13 +9130,13 @@ biolink:RegulatoryRegion a owl:Class ; rdfs:label "regulatory region" ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], @@ -9490,13 +9490,13 @@ biolink:CellularComponent a owl:Class ; biolink:DatasetDistribution a owl:Class ; rdfs:label "dataset distribution" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:distribution_download_url ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:distribution_download_url ], biolink:InformationContentEntity ; skos:definition "an item that holds distribution level information about a dataset." ; @@ -9506,20 +9506,20 @@ biolink:DatasetDistribution a owl:Class ; biolink:DatasetSummary a owl:Class ; rdfs:label "dataset summary" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:source_web_page ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:source_logo ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:source_logo ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:source_logo ], + owl:minCardinality 0 ; + owl:onProperty biolink:source_web_page ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:source_logo ], @@ -9551,21 +9551,21 @@ biolink:GeneToGeneAssociation a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:allValuesFrom biolink:GeneOrGeneProduct ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:object ], biolink:Association ; skos:altLabel "molecular or genetic interaction" ; skos:definition "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; @@ -9647,15 +9647,6 @@ biolink:Protein a owl:Class ; biolink:QuantityValue a owl:Class ; rdfs:label "quantity value" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty biolink:has_unit ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_unit ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_unit ], - [ a owl:Restriction ; owl:allValuesFrom xsd:double ; owl:onProperty biolink:has_numeric_value ], [ a owl:Restriction ; @@ -9664,6 +9655,15 @@ biolink:QuantityValue a owl:Class ; [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_numeric_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_unit ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_unit ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty biolink:has_unit ], biolink:Annotation ; skos:definition "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; skos:inScheme . @@ -9679,15 +9679,9 @@ biolink:SequenceFeatureRelationship a owl:Class ; rdfs:label "sequence feature relationship" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NucleicAcidEntity ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NucleicAcidEntity ; @@ -9695,6 +9689,12 @@ biolink:SequenceFeatureRelationship a owl:Class ; [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NucleicAcidEntity ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "For example, a particular exon is part of a particular transcript or gene" ; skos:exactMatch CHADO:feature_relationship ; @@ -9815,32 +9815,32 @@ biolink:ClinicalAttribute a owl:Class ; biolink:DatasetVersion a owl:Class ; rdfs:label "dataset version" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_dataset ], + [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:ingest_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_distribution ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:ingest_date ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:Dataset ; owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Dataset ; + owl:minCardinality 0 ; owl:onProperty biolink:has_dataset ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DatasetDistribution ; + owl:minCardinality 0 ; owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:ingest_date ], + owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:DatasetDistribution ; owl:onProperty biolink:has_distribution ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_dataset ], + owl:minCardinality 0 ; + owl:onProperty biolink:ingest_date ], biolink:InformationContentEntity ; skos:definition "an item that holds version level information about a dataset." ; skos:inScheme . @@ -9872,11 +9872,8 @@ biolink:FunctionalAssociation a owl:Class ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -9884,8 +9881,11 @@ biolink:FunctionalAssociation a owl:Class ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], biolink:Association ; skos:definition "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; skos:inScheme . @@ -10292,37 +10292,37 @@ biolink:ChemicalMixture a owl:Class ; rdfs:label "chemical mixture" ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:highest_FDA_approval_status ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:highest_FDA_approval_status ], + owl:minCardinality 0 ; + owl:onProperty biolink:is_supplement ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; + owl:onProperty biolink:routes_of_delivery ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ApprovalStatusEnum ; owl:onProperty biolink:drug_regulatory_status_world_wide ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DrugDeliveryEnum ; + owl:onProperty biolink:routes_of_delivery ], [ a owl:Restriction ; owl:allValuesFrom biolink:ApprovalStatusEnum ; owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:is_supplement ], + owl:maxCardinality 1 ; + owl:onProperty biolink:highest_FDA_approval_status ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ApprovalStatusEnum ; + owl:maxCardinality 1 ; owl:onProperty biolink:drug_regulatory_status_world_wide ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:is_supplement ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:routes_of_delivery ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:highest_FDA_approval_status ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugDeliveryEnum ; - owl:onProperty biolink:routes_of_delivery ], biolink:ChemicalEntity ; skos:closeMatch dcid:ChemicalCompound ; skos:definition "A chemical mixture is a chemical entity composed of two or more molecular entities." ; @@ -10348,20 +10348,20 @@ biolink:GeneProductMixin a owl:Class ; biolink:GeneToDiseaseAssociation a owl:Class ; rdfs:label "gene to disease association" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin ], + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], @@ -10369,8 +10369,8 @@ biolink:GeneToDiseaseAssociation a owl:Class ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ], biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; skos:closeMatch dcid:DiseaseGeneAssociation ; skos:exactMatch SIO:000983 ; @@ -10386,37 +10386,37 @@ biolink:MacromolecularMachineMixin a owl:Class ; biolink:MolecularActivity a owl:Class ; rdfs:label "molecular activity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:enabled_by ], + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_input ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:MolecularEntity ; + owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:Occurrent ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_input ], + owl:allValuesFrom biolink:MacromolecularMachineMixin ; + owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_output ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; - owl:onProperty biolink:has_input ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MacromolecularMachineMixin ; - owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MolecularEntity ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_output ], biolink:BiologicalProcessOrActivity ; skos:altLabel "molecular event", @@ -10437,38 +10437,38 @@ biolink:PhysicalEssenceOrOccurrent a owl:Class ; biolink:RetrievalSource a owl:Class ; rdfs:label "retrieval source" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:resource_id ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ResourceRoleEnum ; - owl:onProperty biolink:resource_role ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; + owl:maxCardinality 1 ; owl:onProperty biolink:resource_id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:upstream_resource_ids ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:upstream_resource_ids ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:upstream_resource_ids ], + owl:allValuesFrom biolink:ResourceRoleEnum ; + owl:onProperty biolink:resource_role ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:upstream_resource_ids ], + owl:onProperty biolink:resource_role ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:resource_role ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:resource_id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:resource_role ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:resource_id ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:upstream_resource_ids ], biolink:InformationContentEntity ; skos:definition "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; skos:inScheme . @@ -10823,19 +10823,19 @@ biolink:Genotype a owl:Class ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:allValuesFrom biolink:Zygosity ; owl:onProperty biolink:has_zygosity ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_zygosity ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_zygosity ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], biolink:BiologicalEntity ; skos:definition "An information content entity that describes a genome by specifying the total variation in genomic sequence and/or gene expression, relative to some established background" ; skos:exactMatch , @@ -10930,67 +10930,67 @@ biolink:Entity a owl:Class ; rdfs:label "entity" ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:iri ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:deprecated ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:category ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:description ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:description ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:description ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:deprecated ], + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], + owl:maxCardinality 1 ; + owl:onProperty biolink:iri ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:type ], + owl:onProperty biolink:description ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:description ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; + owl:minCardinality 0 ; owl:onProperty biolink:deprecated ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], + owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:deprecated ], [ a owl:Restriction ; owl:allValuesFrom biolink:Attribute ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:iri ], + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:type ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], linkml:ClassDefinition ; skos:definition "Root Biolink Model class for all things and informational relationships, real or imagined." ; skos:inScheme . @@ -11072,15 +11072,15 @@ biolink:NucleicAcidEntity a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ThingWithTaxon ], biolink:MolecularEntity ; skos:altLabel "genomic entity", "sequence feature" ; @@ -11093,14 +11093,14 @@ biolink:NucleicAcidEntity a owl:Class ; biolink:OrganismalEntity a owl:Class ; rdfs:label "organismal entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_attribute ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SubjectOfInvestigation ], [ a owl:Restriction ; owl:allValuesFrom owl:Thing ; owl:onProperty biolink:has_attribute ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SubjectOfInvestigation ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_attribute ], biolink:BiologicalEntity ; skos:definition "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; skos:exactMatch , @@ -11170,38 +11170,38 @@ biolink:GeneOrGeneProductOrChemicalPartQualifierEnum a owl:Class ; biolink:BiologicalProcessOrActivity a owl:Class ; rdfs:label "biological process or activity" ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_input ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:enabled_by ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:has_output ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 0 ; owl:onProperty biolink:enabled_by ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:Occurrent ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_output ], [ a owl:Restriction ; owl:allValuesFrom biolink:PhysicalEntity ; owl:onProperty biolink:enabled_by ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:has_output ], biolink:BiologicalEntity ; skos:definition "Either an individual molecular activity, or a collection of causally connected molecular activities in a biological system." ; skos:inScheme . @@ -11211,36 +11211,36 @@ biolink:Agent a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:address ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:address ], + [ a owl:Restriction ; + owl:minCardinality 0 ; owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:affiliation ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:address ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:affiliation ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:affiliation ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 0 ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:affiliation ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:address ], + owl:onProperty biolink:id ], biolink:AdministrativeEntity ; skos:altLabel "group" ; skos:definition "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; @@ -11394,10 +11394,10 @@ biolink:DirectionQualifierEnum a owl:Class ; biolink:MolecularEntity a owl:Class ; rdfs:label "molecular entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; + owl:minCardinality 0 ; owl:onProperty biolink:is_metabolite ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:is_metabolite ], [ a owl:Restriction ; owl:maxCardinality 1 ; @@ -11429,41 +11429,41 @@ biolink:BiologicalProcess a owl:Class ; biolink:InformationContentEntity a owl:Class ; rdfs:label "information content entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:rights ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:date ; owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:license ], + owl:onProperty biolink:format ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:license ], + owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:format ], + owl:onProperty biolink:license ], [ a owl:Restriction ; - owl:allValuesFrom xsd:date ; + owl:minCardinality 0 ; owl:onProperty biolink:creation_date ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:rights ], + owl:onProperty biolink:format ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:license ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:format ], + owl:onProperty biolink:license ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:rights ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:creation_date ], + owl:maxCardinality 1 ; + owl:onProperty biolink:rights ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:format ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:license ], + owl:maxCardinality 1 ; + owl:onProperty biolink:creation_date ], biolink:NamedThing ; skos:altLabel "information", "information artefact", @@ -11542,29 +11542,38 @@ biolink:CausalMechanismQualifierEnum a owl:Class ; biolink:Attribute a owl:Class ; rdfs:label "attribute" ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_quantitative_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:has_attribute_type ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_qualitative_value ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:name ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:maxCardinality 1 ; owl:onProperty biolink:iri ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:allValuesFrom biolink:QuantityValue ; owl:onProperty biolink:has_quantitative_value ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quantitative_value ], + owl:minCardinality 1 ; + owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; owl:onProperty biolink:iri ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:has_attribute_type ], + owl:minCardinality 0 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:iri ], @@ -11574,18 +11583,9 @@ biolink:Attribute a owl:Class ; [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_qualitative_value ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_attribute_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:has_qualitative_value ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], biolink:NamedThing ; skos:definition "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; skos:exactMatch SIO:000614 ; @@ -11612,33 +11612,33 @@ biolink:Gene a owl:Class ; rdfs:subClassOf [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GeneOrGeneProduct ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:symbol ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], + owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity ], + owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:symbol ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:OntologyClass ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:xref ], biolink:BiologicalEntity ; skos:broadMatch ; skos:definition "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; @@ -11652,35 +11652,35 @@ biolink:Gene a owl:Class ; biolink:SequenceVariant a owl:Class ; rdfs:label "sequence variant" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_gene ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:OntologyClass ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:id ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:GenomicEntity ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:has_biological_sequence ], @@ -11727,68 +11727,68 @@ biolink:AnatomicalEntity a owl:Class ; biolink:Publication a owl:Class ; rdfs:label "publication" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:authors ], + owl:maxCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:xref ], + owl:onProperty biolink:summary ], [ a owl:Restriction ; owl:allValuesFrom xsd:anyURI ; owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:summary ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:mesh_terms ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:publication_type ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:keywords ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:summary ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], + owl:allValuesFrom biolink:Agent ; + owl:onProperty biolink:authors ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:pages ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:summary ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:publication_type ], + owl:minCardinality 0 ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:minCardinality 0 ; + owl:onProperty biolink:authors ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:name ], + owl:onProperty biolink:pages ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:pages ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:publication_type ], + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:summary ], + owl:onProperty biolink:id ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:keywords ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:id ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:mesh_terms ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:mesh_terms ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Agent ; - owl:onProperty biolink:authors ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:publication_type ], biolink:InformationContentEntity ; skos:definition "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; skos:exactMatch IAO:0000311 ; @@ -11812,56 +11812,56 @@ biolink:BiologicalEntity a owl:Class ; biolink:ChemicalEntity a owl:Class ; rdfs:label "chemical entity" ; rdfs:subClassOf [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], - [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DrugAvailabilityEnum ; + owl:minCardinality 0 ; owl:onProperty biolink:available_from ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:allValuesFrom biolink:ChemicalRole ; owl:onProperty biolink:has_chemical_role ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:trade_name ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:max_tolerated_dose ], + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:trade_name ], + owl:minCardinality 0 ; + owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:trade_name ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:is_toxic ], + owl:allValuesFrom biolink:DrugAvailabilityEnum ; + owl:onProperty biolink:available_from ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom xsd:boolean ; owl:onProperty biolink:is_toxic ], [ a owl:Restriction ; owl:onProperty linkml:mixins ; owl:someValuesFrom biolink:PhysicalEssence ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:is_toxic ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ], + [ a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_chemical_role ], + owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; owl:minCardinality 0 ; + owl:onProperty biolink:has_chemical_role ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:max_tolerated_dose ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:available_from ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:trade_name ], [ a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide ], + owl:maxCardinality 1 ; + owl:onProperty biolink:trade_name ], biolink:NamedThing ; skos:broadMatch STY:T167 ; skos:definition "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; @@ -12002,260 +12002,260 @@ biolink:association_slot a owl:DatatypeProperty ; biolink:Association a owl:Class ; rdfs:label "association" ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_category ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_category_closure ], + [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_category ], + owl:onProperty biolink:type ], [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; - owl:onProperty biolink:timepoint ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:agent_type ], + owl:minCardinality 0 ; + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:primary_knowledge_source ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:p_value ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:float ; - owl:onProperty biolink:adjusted_p_value ], + owl:minCardinality 0 ; + owl:onProperty biolink:type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ], + owl:onProperty biolink:subject_category ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:publications ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualifier ], + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:agent_type ], + owl:allValuesFrom biolink:Publication ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:maxCardinality 1 ; + owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_closure ], + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:qualifiers ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_supporting_studies ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:retrieval_source_ids ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:object_category_closure ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:category ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:adjusted_p_value ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:original_predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_category ], + owl:minCardinality 1 ; + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:original_subject ], + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_category ], + owl:onProperty biolink:original_object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_category_closure ], + owl:onProperty biolink:negated ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:knowledge_source ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:object_category_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:original_object ], + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:type ], + owl:allValuesFrom biolink:Study ; + owl:onProperty biolink:has_supporting_studies ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:negated ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_closure ], + owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_category_closure ], + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; - owl:allValuesFrom biolink:RetrievalSource ; - owl:onProperty biolink:retrieval_source_ids ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:knowledge_level ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_category_closure ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:original_object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Publication ; - owl:onProperty biolink:publications ], + owl:maxCardinality 1 ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_closure ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:original_subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:negated ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:aggregator_knowledge_source ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_category ], + owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:adjusted_p_value ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:time ; + owl:onProperty biolink:timepoint ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_namespace ], + owl:onProperty biolink:has_supporting_studies ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_namespace ], + owl:allValuesFrom xsd:boolean ; + owl:onProperty biolink:negated ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:category ], + owl:maxCardinality 1 ; + owl:onProperty biolink:qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:knowledge_source ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AgentTypeEnum ; - owl:onProperty biolink:agent_type ], + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:OntologyClass ; owl:onProperty biolink:object_category ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:subject_category ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:original_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualifiers ], + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; - owl:allValuesFrom xsd:boolean ; - owl:onProperty biolink:negated ], + owl:minCardinality 0 ; + owl:onProperty biolink:publications ], [ a owl:Restriction ; - owl:allValuesFrom biolink:EvidenceType ; - owl:onProperty biolink:has_evidence ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_category ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Study ; - owl:onProperty biolink:has_supporting_studies ], + owl:onProperty biolink:negated ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:type ], + owl:onProperty biolink:has_evidence ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 0 ; owl:onProperty biolink:subject_namespace ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_namespace ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:p_value ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:KnowledgeLevelEnum ; - owl:onProperty biolink:knowledge_level ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_label_closure ], + owl:onProperty biolink:subject_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_label_closure ], + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:adjusted_p_value ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:original_subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:knowledge_source ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:object_label_closure ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:original_object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_namespace ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:allValuesFrom biolink:AgentTypeEnum ; + owl:onProperty biolink:agent_type ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; + owl:allValuesFrom biolink:EvidenceType ; + owl:onProperty biolink:has_evidence ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:primary_knowledge_source ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_namespace ], + owl:allValuesFrom biolink:RetrievalSource ; + owl:onProperty biolink:retrieval_source_ids ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:knowledge_source ], + owl:allValuesFrom biolink:KnowledgeLevelEnum ; + owl:onProperty biolink:knowledge_level ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_label_closure ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:p_value ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:aggregator_knowledge_source ], + owl:onProperty biolink:knowledge_source ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_namespace ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:original_object ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:timepoint ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_evidence ], + owl:maxCardinality 1 ; + owl:onProperty biolink:knowledge_source ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:agent_type ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:original_subject ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:original_predicate ], + owl:onProperty biolink:retrieval_source_ids ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:agent_type ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:knowledge_level ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_closure ], + owl:allValuesFrom xsd:float ; + owl:onProperty biolink:p_value ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:primary_knowledge_source ], + owl:minCardinality 0 ; + owl:onProperty biolink:qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualifiers ], biolink:Entity ; skos:definition "A typed association between two entities, supported by evidence" ; skos:exactMatch OBAN:association, @@ -12275,14 +12275,14 @@ biolink:related_to_at_instance_level a owl:DatatypeProperty, biolink:NamedThing a owl:Class ; rdfs:label "named thing" ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], + owl:maxCardinality 1 ; + owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:synonym ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:full_name ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:full_name ], @@ -12290,20 +12290,20 @@ biolink:NamedThing a owl:Class ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:provided_by ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:category ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:full_name ], + owl:minCardinality 0 ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:synonym ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:full_name ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:minCardinality 1 ; owl:onProperty biolink:category ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], [ a owl:Restriction ; owl:minCardinality 0 ; owl:onProperty biolink:provided_by ], @@ -12358,405 +12358,527 @@ biolink:subject a owl:ObjectProperty ; owl:annotatedSource ; skos:inScheme . +[] a owl:Restriction ; + rdfs:subClassOf biolink:Snv ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Snv . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PhenotypicFeature ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhenotypicFeature . + [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:Outcome ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ] ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexChemicalExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexChemicalExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:TextMiningResult ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TextMiningResult . + owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; + rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . + owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:FoodAdditive ; + rdfs:subClassOf biolink:InformationContentEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FoodAdditive . + owl:someValuesFrom biolink:InformationContentEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Serial ; + rdfs:subClassOf biolink:ClinicalIntervention ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Serial . + owl:someValuesFrom biolink:ClinicalIntervention . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhysicalEntity ; + rdfs:subClassOf biolink:ProteinFamily ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysicalEntity . + owl:someValuesFrom biolink:ProteinFamily . [] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntity . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; + rdfs:subClassOf biolink:SequenceVariant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . + owl:someValuesFrom biolink:SequenceVariant . [] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; + rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptionFactorBindingSite . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:in_taxon_label ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:in_taxon ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:in_taxon_label ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:in_taxon_label ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ThingWithTaxon . + owl:someValuesFrom biolink:NucleicAcidSequenceMotif . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhysiologicalProcess ; + rdfs:subClassOf biolink:WebPage ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhysiologicalProcess . + owl:someValuesFrom biolink:WebPage . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralExposure ; + rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralExposure . + owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToDiseaseAssociation ; + rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToDiseaseAssociation . + owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:PosttranslationalModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:PosttranslationalModification . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:CellLine ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:MaterialSample ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . + owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:CommonDataElement ; + rdfs:subClassOf biolink:DrugLabel ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CommonDataElement . + owl:someValuesFrom biolink:DrugLabel . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], + rdfs:subClassOf biolink:DatasetVersion ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DatasetVersion . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:TaxonToTaxonAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:TaxonToTaxonAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ClinicalModifier ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ClinicalModifier . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BiologicalProcess ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BiologicalProcess . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PhysicalEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhysicalEntity . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Bacterium ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Bacterium . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Polypeptide ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Polypeptide . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PhysicalEssence . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:phenotypic_state ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:phenotypic_state ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:AnatomicalEntity ; + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:allValuesFrom biolink:OntologyClass ; + owl:onProperty biolink:quantifier_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], + owl:onProperty biolink:stage_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:LifeStage ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:onProperty biolink:expression_site ], [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:stage_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ] ; + owl:onProperty biolink:quantifier_qualifier ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalStructure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToPathwayAssociation . + owl:someValuesFrom biolink:GeneExpressionMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChiSquaredAnalysisResult . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:double ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_quotient ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:integer ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_count ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_percentage ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_total ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_quotient ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:SiRNA ; + rdfs:subClassOf biolink:RetrievalSource ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SiRNA . + owl:someValuesFrom biolink:RetrievalSource . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetVersion ; + rdfs:subClassOf biolink:GeographicExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetVersion . + owl:someValuesFrom biolink:GeographicExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneFamily ; + rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneFamily . + owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Outcome ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:maxCardinality 1 ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToOutcomeAssociationMixin . + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:SeverityValue ; + rdfs:subClassOf biolink:VariantToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SeverityValue . + owl:someValuesFrom biolink:VariantToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicQuality ; + rdfs:subClassOf biolink:ClinicalAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicQuality . + owl:someValuesFrom biolink:ClinicalAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntity ; + rdfs:subClassOf biolink:BiologicalSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntity . + owl:someValuesFrom biolink:BiologicalSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:Cohort ; + rdfs:subClassOf biolink:ProteinIsoform ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cohort . + owl:someValuesFrom biolink:ProteinIsoform . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularOrganism ; + rdfs:subClassOf biolink:ConfidenceLevel ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularOrganism . + owl:someValuesFrom biolink:ConfidenceLevel . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; + rdfs:subClassOf biolink:DrugToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . + owl:someValuesFrom biolink:DrugToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:NoncodingRNAProduct ; + rdfs:subClassOf biolink:ProcessedMaterial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NoncodingRNAProduct . + owl:someValuesFrom biolink:ProcessedMaterial . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; + rdfs:subClassOf biolink:Transcript ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . + owl:someValuesFrom biolink:Transcript . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:StudyResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:StudyResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genome ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:Occurrent . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Human ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genome . + owl:someValuesFrom biolink:Human . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxon ; + rdfs:subClassOf biolink:ChiSquaredAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxon . + owl:someValuesFrom biolink:ChiSquaredAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:PhysiologicalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:PhysiologicalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom ; + owl:onProperty biolink:frequency_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:FrequencyQualifierMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToGoTermAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . + owl:someValuesFrom biolink:GeneToGoTermAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFeature ; + rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFeature . + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetDistribution ; + rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetDistribution . + owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehavioralFeature ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehavioralFeature . + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; + rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . + owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:WebPage ; + rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:WebPage . + owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:GrossAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . + owl:someValuesFrom biolink:GrossAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; + rdfs:subClassOf biolink:GeographicLocation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . + owl:someValuesFrom biolink:GeographicLocation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; + rdfs:subClassOf biolink:NucleicAcidEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . + owl:someValuesFrom biolink:NucleicAcidEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:PosttranslationalModification ; + rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PosttranslationalModification . + owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalRole ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathognomonicityQuantifier . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ConceptCountAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalRole . + owl:someValuesFrom biolink:ConceptCountAnalysisResult . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ActivityAndBehavior . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Patent ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Patent . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneRegulatesGeneAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneRegulatesGeneAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], @@ -12764,794 +12886,831 @@ biolink:subject a owl:ObjectProperty ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Drug ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:Disease ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DrugToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessedMaterial ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessedMaterial . + owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Snv ; + rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Snv . + owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneHasVariantThatContributesToDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneHasVariantThatContributesToDiseaseAssociation . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:Hospitalization ; + rdfs:subClassOf biolink:RegulatoryRegion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Hospitalization . + owl:someValuesFrom biolink:RegulatoryRegion . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; + rdfs:subClassOf biolink:CommonDataElement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalAnatomicalExposure . + owl:someValuesFrom biolink:CommonDataElement . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:BiologicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:BiologicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; + rdfs:subClassOf biolink:AdministrativeEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . + owl:someValuesFrom biolink:AdministrativeEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:DatasetSummary ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:DatasetSummary . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:species_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . + owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . + +[] a owl:Restriction ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:PathologicalEntityMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Study ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Study . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:RNAProduct ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RNAProduct . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Serial ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Serial . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Behavior ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Behavior . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Cell ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Cell . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Article ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Article . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:GeneticInheritance ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:GeneticInheritance . [] a owl:Restriction ; - rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; + rdfs:subClassOf biolink:Gene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . + owl:someValuesFrom biolink:Gene . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalSex ; + rdfs:subClassOf biolink:FunctionalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalSex . + owl:someValuesFrom biolink:FunctionalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicSequenceLocalization ; + rdfs:subClassOf biolink:CellularOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicSequenceLocalization . + owl:someValuesFrom biolink:CellularOrganism . [] a owl:Restriction ; - rdfs:subClassOf biolink:Pathway ; + rdfs:subClassOf biolink:Virus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Pathway . + owl:someValuesFrom biolink:Virus . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:ChemicalToPathwayAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:ChemicalToPathwayAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Case ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Case . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:time ; - owl:onProperty biolink:timepoint ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:timepoint ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ExposureEvent . + owl:someValuesFrom biolink:SpecificityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneAssociation ; + rdfs:subClassOf biolink:SeverityValue ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneAssociation . + owl:someValuesFrom biolink:SeverityValue . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalExposure ; + rdfs:subClassOf biolink:Haplotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalExposure . + owl:someValuesFrom biolink:Haplotype . [] a owl:Restriction ; - rdfs:subClassOf biolink:Book ; + rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Book . + owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularComplex ; + rdfs:subClassOf biolink:JournalArticle ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularComplex . + owl:someValuesFrom biolink:JournalArticle . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; + rdfs:subClassOf biolink:Activity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . + owl:someValuesFrom biolink:Activity . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Occurrent . + rdfs:subClassOf biolink:Pathway ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Pathway . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicSex ; + rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicSex . + owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocationAtTime ; + rdfs:subClassOf biolink:ClinicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocationAtTime . + owl:someValuesFrom biolink:ClinicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToVariantAssociation ; + rdfs:subClassOf biolink:MolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToVariantAssociation . + owl:someValuesFrom biolink:MolecularMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:TranscriptToGeneRelationship ; + rdfs:subClassOf biolink:ChemicalEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TranscriptToGeneRelationship . + owl:someValuesFrom biolink:ChemicalEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; + rdfs:subClassOf biolink:Event ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . + owl:someValuesFrom biolink:Event . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:frequency_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom ; - owl:onProperty biolink:frequency_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQualifierMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DrugExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicAttribute ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicAttribute . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugToGeneInteractionExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Invertebrate ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Invertebrate . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToPhenotypicFeatureAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToPhenotypicFeatureAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceAssociation . + owl:someValuesFrom biolink:VariantToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalAttribute ; + rdfs:subClassOf biolink:TextMiningResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalAttribute . + owl:someValuesFrom biolink:TextMiningResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleosomeModification ; + rdfs:subClassOf biolink:GenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleosomeModification . + owl:someValuesFrom biolink:GenotypicSex . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalEntity . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:xref ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:synonym ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:synonym ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneProductMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyPopulation ; + rdfs:subClassOf biolink:EvidenceType ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyPopulation . + owl:someValuesFrom biolink:EvidenceType . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; + rdfs:subClassOf biolink:PlanetaryEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . + owl:someValuesFrom biolink:PlanetaryEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:Dataset ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:Dataset . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; + rdfs:subClassOf biolink:Publication ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . + owl:someValuesFrom biolink:Publication . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypicSex ; + rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypicSex . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssenceOrOccurrent . + owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalTrial ; + rdfs:subClassOf biolink:MolecularActivity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalTrial . + owl:someValuesFrom biolink:MolecularActivity . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . + owl:someValuesFrom biolink:SubjectOfInvestigation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismAttribute ; + rdfs:subClassOf biolink:DruggableGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismAttribute . + owl:someValuesFrom biolink:DruggableGeneToDiseaseAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:disease_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_direction_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:disease_context_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:subject_aspect_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DirectionQualifierEnum ; - owl:onProperty biolink:object_direction_qualifier ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:qualified_predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:disease_context_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_aspect_qualifier ], + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_aspect_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject_direction_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:qualified_predicate ] ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . + owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Protein ; + rdfs:subClassOf biolink:Procedure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Protein . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SensitivityQuantifier . + owl:someValuesFrom biolink:Procedure . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinDomain ; + rdfs:subClassOf biolink:StudyVariable ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinDomain . + owl:someValuesFrom biolink:StudyVariable . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:object_specialization_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:anatomical_context_qualifier ], - [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:subject_specialization_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:object_specialization_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:disease_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:disease_context_qualifier ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:anatomical_context_qualifier ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject_specialization_qualifier ], + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:subject_specialization_qualifier ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object_specialization_qualifier ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:disease_context_qualifier ] ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyVariable ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneProductIsoformMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Mammal ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyVariable . + owl:someValuesFrom biolink:Mammal . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:IndividualOrganism ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:IndividualOrganism . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToGeneAssociation ; + rdfs:subClassOf biolink:Entity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToGeneAssociation . + owl:someValuesFrom biolink:Entity . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSample ; + rdfs:subClassOf biolink:DrugToGeneInteractionExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSample . + owl:someValuesFrom biolink:DrugToGeneInteractionExposure . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:CodingSequence ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CodingSequence . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:RNAProductIsoform ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:RNAProductIsoform . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismalEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismalEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:AnatomicalEntity ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:AnatomicalEntity . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GenomicEntity . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:BehavioralExposure ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:BehavioralExposure . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:PhenotypicFeature ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:BiologicalSex ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:SequenceVariant ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ] ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:VariantToEntityAssociationMixin . + owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ClinicalTrial ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ClinicalTrial . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonAssociation ; + rdfs:subClassOf biolink:GeneToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonAssociation . + owl:someValuesFrom biolink:GeneToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProduct ; + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:object ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Fungus ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProduct . + owl:someValuesFrom biolink:Fungus . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneHomologyAssociation ; + rdfs:subClassOf biolink:GenotypeToVariantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneHomologyAssociation . + owl:someValuesFrom biolink:GenotypeToVariantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Article ; + rdfs:subClassOf biolink:Protein ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Article . + owl:someValuesFrom biolink:Protein . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; + rdfs:subClassOf biolink:Drug ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . + owl:someValuesFrom biolink:Drug . [] a owl:Restriction ; - rdfs:subClassOf biolink:AnatomicalEntity ; + rdfs:subClassOf biolink:GeneToGeneProductRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AnatomicalEntity . + owl:someValuesFrom biolink:GeneToGeneProductRelationship . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:anyURI ; - owl:onProperty biolink:xref ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:synonym ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:synonym ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductMixin . + rdfs:subClassOf biolink:MacromolecularComplex ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MacromolecularComplex . [] a owl:Restriction ; - rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:MolecularEntity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:MolecularEntity . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; + owl:allValuesFrom biolink:Drug ; + owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociationMixin . + owl:someValuesFrom biolink:DrugToEntityAssociationMixin . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct . + rdfs:subClassOf biolink:OrganismAttribute ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:OrganismAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:RegulatoryRegion ; + rdfs:subClassOf biolink:ProteinDomain ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RegulatoryRegion . + owl:someValuesFrom biolink:ProteinDomain . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellularComponent ; + rdfs:subClassOf biolink:GenotypeToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellularComponent . + owl:someValuesFrom biolink:GenotypeToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Entity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Entity . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:GeneOrGeneProduct . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicLocation ; + rdfs:subClassOf biolink:PairwiseMolecularInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicLocation . + owl:someValuesFrom biolink:PairwiseMolecularInteraction . [] a owl:Restriction ; - rdfs:subClassOf biolink:Vertebrate ; + rdfs:subClassOf biolink:LifeStage ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Vertebrate . + owl:someValuesFrom biolink:LifeStage . [] a owl:Restriction ; - rdfs:subClassOf biolink:ComplexMolecularMixture ; + rdfs:subClassOf biolink:BiologicalProcessOrActivity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ComplexMolecularMixture . + owl:someValuesFrom biolink:BiologicalProcessOrActivity . [] a owl:Restriction ; - rdfs:subClassOf biolink:Dataset ; + rdfs:subClassOf biolink:Genotype ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Dataset . + owl:someValuesFrom biolink:Genotype . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:EnvironmentalProcess ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:EnvironmentalProcess . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToParticipantAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToParticipantAssociation . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom biolink:MaterialSample ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MaterialSampleToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalEntity ; + rdfs:subClassOf biolink:GeneToExpressionSiteAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalEntity . + owl:someValuesFrom biolink:GeneToExpressionSiteAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Drug ; + rdfs:subClassOf biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Drug . + owl:someValuesFrom biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DatasetSummary ; + rdfs:subClassOf biolink:Phenomenon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DatasetSummary . + owl:someValuesFrom biolink:Phenomenon . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntity ; + rdfs:subClassOf biolink:Exon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntity . + owl:someValuesFrom biolink:Exon . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneAssociation . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:has_biological_sequence ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:has_biological_sequence ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EpigenomicEntity . [] a owl:Restriction ; - rdfs:subClassOf biolink:AccessibleDnaRegion ; + rdfs:subClassOf biolink:GeneToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AccessibleDnaRegion . + owl:someValuesFrom biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidSequenceMotif ; + rdfs:subClassOf biolink:PhenotypicSex ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidSequenceMotif . + owl:someValuesFrom biolink:PhenotypicSex . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:BiologicalSex ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:PhenotypicFeature ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:sex_qualifier ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:sex_qualifier ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhenotypicFeatureToEntityAssociationMixin . + rdfs:subClassOf biolink:PhenotypicFeatureToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToDiseaseAssociation ; + rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToDiseaseAssociation . + owl:someValuesFrom biolink:ChemicalToChemicalAssociation . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_gene_or_gene_product ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:Gene ; - owl:onProperty biolink:has_gene_or_gene_product ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneGroupingMixin . + rdfs:subClassOf biolink:CaseToPhenotypicFeatureAssociation ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:CaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MicroRNA ; + rdfs:subClassOf biolink:SiRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MicroRNA . + owl:someValuesFrom biolink:SiRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalProcess ; + rdfs:subClassOf biolink:PopulationOfIndividualOrganisms ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalProcess . + owl:someValuesFrom biolink:PopulationOfIndividualOrganisms . [] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:RelationshipQuantifier . + rdfs:subClassOf biolink:Device ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Device . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation ; + rdfs:subClassOf biolink:TranscriptToGeneRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . + owl:someValuesFrom biolink:TranscriptToGeneRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalAffectsGeneAssociation ; + rdfs:subClassOf biolink:GenotypeToGenotypePartAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalAffectsGeneAssociation . + owl:someValuesFrom biolink:GenotypeToGenotypePartAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Publication ; + rdfs:subClassOf biolink:GenomicBackgroundExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Publication . + owl:someValuesFrom biolink:GenomicBackgroundExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; + rdfs:subClassOf biolink:LogOddsAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . + owl:someValuesFrom biolink:LogOddsAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenomicEntity . + rdfs:subClassOf biolink:Onset ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Onset . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiagnosticAid ; + rdfs:subClassOf biolink:TranscriptionFactorBindingSite ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiagnosticAid . + owl:someValuesFrom biolink:TranscriptionFactorBindingSite . [] a owl:Restriction ; - rdfs:subClassOf biolink:AdministrativeEntity ; + rdfs:subClassOf biolink:GeneToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:AdministrativeEntity . + owl:someValuesFrom biolink:GeneToGeneAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Phenomenon ; + rdfs:subClassOf biolink:NucleosomeModification ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Phenomenon . + owl:someValuesFrom biolink:NucleosomeModification . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularEntity ; + rdfs:subClassOf biolink:OrganismToOrganismAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularEntity . + owl:someValuesFrom biolink:OrganismToOrganismAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; + rdfs:subClassOf biolink:Agent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . + owl:someValuesFrom biolink:Agent . [] a owl:Restriction ; - rdfs:subClassOf biolink:Association ; + rdfs:subClassOf biolink:VariantToGeneAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Association . + owl:someValuesFrom biolink:VariantToGeneAssociation . [] a owl:Restriction ; rdfs:subClassOf biolink:AnatomicalEntityToAnatomicalEntityAssociation ; @@ -13559,33 +13718,40 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:AnatomicalEntityToAnatomicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:NamedThing ; + rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NamedThing . + owl:someValuesFrom biolink:EnvironmentalFoodContaminant . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:MaterialSample ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:MaterialSample . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Attribute ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Attribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:ConfidenceLevel ; + rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConfidenceLevel . + owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalIntervention ; + rdfs:subClassOf biolink:NoncodingRNAProduct ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalIntervention . + owl:someValuesFrom biolink:NoncodingRNAProduct . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:ExposureEvent ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:object ], @@ -13596,359 +13762,345 @@ biolink:subject a owl:ObjectProperty ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneToEntityAssociationMixin . + owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseMolecularInteraction ; + rdfs:subClassOf biolink:PathologicalAnatomicalStructure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseMolecularInteraction . + owl:someValuesFrom biolink:PathologicalAnatomicalStructure . [] a owl:Restriction ; - rdfs:subClassOf biolink:PopulationToPopulationAssociation ; + rdfs:subClassOf biolink:Book ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PopulationToPopulationAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SpecificityQuantifier . + owl:someValuesFrom biolink:Book . [] a owl:Restriction ; - rdfs:subClassOf biolink:PreprintPublication ; + rdfs:subClassOf biolink:CellLine ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PreprintPublication . + owl:someValuesFrom biolink:CellLine . [] a owl:Restriction ; - rdfs:subClassOf biolink:Mammal ; + rdfs:subClassOf biolink:EnvironmentalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Mammal . + owl:someValuesFrom biolink:EnvironmentalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Attribute ; + rdfs:subClassOf biolink:GeneToGeneCoexpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Attribute . + owl:someValuesFrom biolink:GeneToGeneCoexpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:LogOddsAnalysisResult ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LogOddsAnalysisResult . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:Exon ; + rdfs:subClassOf biolink:GeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Exon . + owl:someValuesFrom biolink:GeneToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Human ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Human . + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:time ; + owl:onProperty biolink:timepoint ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:timepoint ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ExposureEvent . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToPathwayAssociation ; + rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToPathwayAssociation . + owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:GeneFamily ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:GeneFamily . [] a owl:Restriction ; - rdfs:subClassOf biolink:StudyResult ; + rdfs:subClassOf biolink:Food ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:StudyResult . + owl:someValuesFrom biolink:Food . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneFamilyAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneFamilyAssociation . + rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Case ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:CaseToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneticInheritance ; + rdfs:subClassOf biolink:Association ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneticInheritance . + owl:someValuesFrom biolink:Association . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; + rdfs:subClassOf biolink:OrganismTaxon ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:OrganismTaxon . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcess ; + rdfs:subClassOf biolink:Hospitalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcess . + owl:someValuesFrom biolink:Hospitalization . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismToOrganismAssociation ; + rdfs:subClassOf biolink:ExonToTranscriptRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismToOrganismAssociation . + owl:someValuesFrom biolink:ExonToTranscriptRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:Disease ; + rdfs:subClassOf biolink:SequenceFeatureRelationship ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Disease . + owl:someValuesFrom biolink:SequenceFeatureRelationship . [] a owl:Restriction ; - rdfs:subClassOf biolink:EnvironmentalFoodContaminant ; + rdfs:subClassOf biolink:ObservedExpectedFrequencyAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EnvironmentalFoodContaminant . + owl:someValuesFrom biolink:ObservedExpectedFrequencyAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinIsoform ; + rdfs:subClassOf biolink:FoodAdditive ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinIsoform . + owl:someValuesFrom biolink:FoodAdditive . [] a owl:Restriction ; - rdfs:subClassOf biolink:Genotype ; + rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Genotype . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . + owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProcessRegulatesProcessAssociation ; + rdfs:subClassOf biolink:MicroRNA ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProcessRegulatesProcessAssociation . + owl:someValuesFrom biolink:MicroRNA . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToDiseaseAssociation ; + rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToDiseaseAssociation . + owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:MacromolecularMachineToBiologicalProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:MacromolecularMachineToBiologicalProcessAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ProteinFamily ; + rdfs:subClassOf biolink:DatasetDistribution ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ProteinFamily . + owl:someValuesFrom biolink:DatasetDistribution . [] a owl:Restriction ; - rdfs:subClassOf biolink:LifeStage ; + rdfs:subClassOf biolink:SocioeconomicExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:LifeStage . + owl:someValuesFrom biolink:SocioeconomicExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Fungus ; + rdfs:subClassOf biolink:PhenotypicFeatureToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Fungus . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneProductIsoformMixin . + owl:someValuesFrom biolink:PhenotypicFeatureToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalDerivationAssociation ; + rdfs:subClassOf biolink:GenomicSequenceLocalization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalDerivationAssociation . + owl:someValuesFrom biolink:GenomicSequenceLocalization . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceFeatureRelationship ; + rdfs:subClassOf biolink:VariantToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceFeatureRelationship . + owl:someValuesFrom biolink:VariantToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToEnvironmentAssociation ; + rdfs:subClassOf biolink:BehaviorToBehavioralFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToEnvironmentAssociation . + owl:someValuesFrom biolink:BehaviorToBehavioralFeatureAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:OrganismTaxon ; - owl:onProperty biolink:species_context_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:object_aspect_qualifier ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:species_context_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ] ; + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GeneRegulatesGeneAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneRegulatesGeneAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcessOrActivity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcessOrActivity . + owl:someValuesFrom biolink:FeatureOrDiseaseQualifiersToEntityMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularMixture ; + rdfs:subClassOf biolink:MacromolecularMachineToCellularComponentAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularMixture . + owl:someValuesFrom biolink:MacromolecularMachineToCellularComponentAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:BookChapter ; + rdfs:subClassOf biolink:VariantAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BookChapter . + owl:someValuesFrom biolink:VariantAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; + rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . + owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReagentTargetedGene ; + rdfs:subClassOf biolink:ContributorAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReagentTargetedGene . + owl:someValuesFrom biolink:ContributorAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Polypeptide ; + rdfs:subClassOf biolink:BehavioralFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Polypeptide . + owl:someValuesFrom biolink:BehavioralFeature . [] a owl:Restriction ; - rdfs:subClassOf biolink:CodingSequence ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CodingSequence . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:ChemicalEntityOrProteinOrPolypeptide . [] a owl:Restriction ; - rdfs:subClassOf biolink:Bacterium ; + rdfs:subClassOf biolink:VariantToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Bacterium . + owl:someValuesFrom biolink:VariantToPopulationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalMeasurement ; + rdfs:subClassOf biolink:PathologicalProcessExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalMeasurement . + owl:someValuesFrom biolink:PathologicalProcessExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Transcript ; + rdfs:subClassOf biolink:Invertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Transcript . + owl:someValuesFrom biolink:Invertebrate . [] a owl:Restriction ; - rdfs:subClassOf biolink:Case ; + rdfs:subClassOf biolink:ExposureEventToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Case . + owl:someValuesFrom biolink:ExposureEventToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:JournalArticle ; + rdfs:subClassOf biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:JournalArticle . + owl:someValuesFrom biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:RNAProductIsoform ; + rdfs:subClassOf biolink:BioticExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RNAProductIsoform . + owl:someValuesFrom biolink:BioticExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariant ; + rdfs:subClassOf biolink:CellularComponent ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariant . + owl:someValuesFrom biolink:CellularComponent . [] a owl:Restriction ; - rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; + rdfs:subClassOf biolink:DiagnosticAid ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . + owl:someValuesFrom biolink:DiagnosticAid . [] a owl:Restriction ; - rdfs:subClassOf biolink:MacromolecularMachineToMolecularActivityAssociation ; + rdfs:subClassOf biolink:SocioeconomicAttribute ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MacromolecularMachineToMolecularActivityAssociation . + owl:someValuesFrom biolink:SocioeconomicAttribute . [] a owl:Restriction ; - rdfs:subClassOf biolink:Zygosity ; + rdfs:subClassOf biolink:ProcessRegulatesProcessAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Zygosity . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathognomonicityQuantifier . + owl:someValuesFrom biolink:ProcessRegulatesProcessAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:in_taxon ], + [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_biological_sequence ], + owl:onProperty biolink:in_taxon_label ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:has_biological_sequence ], + owl:minCardinality 0 ; + owl:onProperty biolink:in_taxon_label ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:in_taxon ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:has_biological_sequence ] ; + owl:onProperty biolink:in_taxon ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EpigenomicEntity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismalEntityAsAModelOfDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismalEntityAsAModelOfDiseaseAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:GrossAnatomicalStructure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GrossAnatomicalStructure . + owl:someValuesFrom biolink:ThingWithTaxon . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; @@ -13956,190 +14108,154 @@ biolink:subject a owl:ObjectProperty ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:disease_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; - owl:onProperty biolink:subject ], + owl:minCardinality 1 ; + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_specialization_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_specialization_qualifier ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_specialization_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:DiseaseToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:subject_specialization_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom xsd:anyURI ; + owl:onProperty biolink:object_specialization_qualifier ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Genotype ; - owl:onProperty biolink:subject ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:minCardinality 0 ; + owl:onProperty biolink:disease_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:anatomical_context_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:object_specialization_qualifier ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:disease_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:subject ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:SmallMolecule ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SmallMolecule . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalEntityAssessesNamedThingAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalEntityAssessesNamedThingAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineAsAModelOfDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineAsAModelOfDiseaseAssociation . + owl:someValuesFrom biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Plant ; + rdfs:subClassOf biolink:ReactionToParticipantAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Plant . + owl:someValuesFrom biolink:ReactionToParticipantAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Virus ; + rdfs:subClassOf biolink:VariantToGeneExpressionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Virus . + owl:someValuesFrom biolink:VariantToGeneExpressionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Cell ; + rdfs:subClassOf biolink:Zygosity ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Cell . + owl:someValuesFrom biolink:Zygosity . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PathologicalEntityMixin . + owl:someValuesFrom biolink:Outcome . [] a owl:Restriction ; - rdfs:subClassOf biolink:TaxonToTaxonAssociation ; + rdfs:subClassOf biolink:ExposureEventToOutcomeAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:TaxonToTaxonAssociation . + owl:someValuesFrom biolink:ExposureEventToOutcomeAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseToExposureEventAssociation ; + rdfs:subClassOf biolink:GeneAsAModelOfDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseToExposureEventAssociation . + owl:someValuesFrom biolink:GeneAsAModelOfDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:SequenceVariantModulatesTreatmentAssociation ; + rdfs:subClassOf biolink:Disease ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SequenceVariantModulatesTreatmentAssociation . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:double ; - owl:onProperty biolink:has_percentage ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_count ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_percentage ], + owl:someValuesFrom biolink:Disease . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:PathologicalProcess ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:PathologicalProcess . + +[] a owl:Restriction ; + rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:id ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:has_total ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:id ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_total ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:has_quotient ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:integer ; - owl:onProperty biolink:has_count ] ; + owl:onProperty biolink:id ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:FrequencyQuantifier . + owl:someValuesFrom biolink:OntologyClass . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; + owl:allValuesFrom biolink:OrganismTaxon ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:ExposureEvent ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; - owl:maxCardinality 1 ; + owl:minCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToExposureEventAssociationMixin . + owl:someValuesFrom biolink:OrganismTaxonToEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:MolecularActivityToPathwayAssociation ; + rdfs:subClassOf biolink:Vertebrate ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:MolecularActivityToPathwayAssociation . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:Outcome . + owl:someValuesFrom biolink:Vertebrate . [] a owl:Restriction ; rdfs:subClassOf biolink:Treatment ; @@ -14147,45 +14263,35 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:Treatment . [] a owl:Restriction ; - rdfs:subClassOf biolink:RetrievalSource ; + rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RetrievalSource . + owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . + +[] a owl:Restriction ; + rdfs:subClassOf biolink:Plant ; + owl:onProperty biolink:category ; + owl:someValuesFrom biolink:Plant . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:name ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:name ], + owl:allValuesFrom biolink:Gene ; + owl:onProperty biolink:has_gene_or_gene_product ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:name ] ; + owl:onProperty biolink:has_gene_or_gene_product ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:MacromolecularMachineMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:DrugLabel ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DrugLabel . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:EvidenceType ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EvidenceType . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalModifier ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalModifier . + owl:someValuesFrom biolink:GeneGroupingMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:FunctionalAssociation ; + rdfs:subClassOf biolink:ChemicalRole ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:FunctionalAssociation . + owl:someValuesFrom biolink:ChemicalRole . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; owl:allValuesFrom xsd:string ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; @@ -14193,295 +14299,187 @@ biolink:subject a owl:ObjectProperty ; owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:CellLine ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:GeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CellLineToEntityAssociationMixin . + owl:someValuesFrom biolink:GeneToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:EntityToPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:ClinicalMeasurement ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:EntityToPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:ClinicalMeasurement . [] a owl:Restriction ; - rdfs:subClassOf biolink:ContributorAssociation ; + rdfs:subClassOf biolink:Cohort ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ContributorAssociation . + owl:someValuesFrom biolink:Cohort . [] a owl:Restriction ; - rdfs:subClassOf biolink:SocioeconomicExposure ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:SocioeconomicExposure . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonInteraction . [] a owl:Restriction ; - rdfs:subClassOf biolink:ExonToTranscriptRelationship ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ExonToTranscriptRelationship . + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:SensitivityQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; + rdfs:subClassOf biolink:ComplexMolecularMixture ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . + owl:someValuesFrom biolink:ComplexMolecularMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenomicBackgroundExposure ; + rdfs:subClassOf biolink:PopulationToPopulationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenomicBackgroundExposure . + owl:someValuesFrom biolink:PopulationToPopulationAssociation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:LifeStage ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:AnatomicalEntity ; - owl:onProperty biolink:expression_site ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:DiseaseOrPhenotypicFeature ; - owl:onProperty biolink:phenotypic_state ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:minCardinality 0 ; - owl:onProperty biolink:stage_qualifier ], - [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:quantifier_qualifier ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:OntologyClass ; - owl:onProperty biolink:quantifier_qualifier ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:phenotypic_state ], + owl:minCardinality 0 ; + owl:onProperty biolink:disease_context_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:stage_qualifier ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:expression_site ], + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:expression_site ], + owl:onProperty biolink:qualified_predicate ], [ a owl:Restriction ; owl:minCardinality 0 ; - owl:onProperty biolink:phenotypic_state ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneExpressionMixin . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:maxCardinality 1 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Disease ; + owl:onProperty biolink:disease_context_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalEntityToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:Case ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:subject_aspect_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:subject_direction_qualifier ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:minCardinality 0 ; + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_direction_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:object_aspect_qualifier ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], - [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:predicate ], + owl:onProperty biolink:disease_context_qualifier ], [ a owl:Restriction ; - owl:minCardinality 1 ; - owl:onProperty biolink:subject ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:CaseToEntityAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:InformationContentEntityToNamedThingAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:InformationContentEntityToNamedThingAssociation . + owl:allValuesFrom biolink:DirectionQualifierEnum ; + owl:onProperty biolink:subject_direction_qualifier ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:EntityToFeatureOrDiseaseQualifiersMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation ; + rdfs:subClassOf biolink:DrugExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . + owl:someValuesFrom biolink:DrugExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGoTermAssociation ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGoTermAssociation . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ReactionToCatalystAssociation ; + rdfs:subClassOf biolink:MaterialSampleDerivationAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ReactionToCatalystAssociation . + owl:someValuesFrom biolink:MaterialSampleDerivationAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Procedure ; + rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Procedure . + owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Agent ; + rdfs:subClassOf biolink:DiseaseToPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Agent . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ActivityAndBehavior . + owl:someValuesFrom biolink:DiseaseToPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; + rdfs:subClassOf biolink:PhenotypicQuality ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . + owl:someValuesFrom biolink:PhenotypicQuality . [] a owl:Restriction ; - rdfs:subClassOf biolink:PhenotypicFeature ; + rdfs:subClassOf biolink:NamedThing ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PhenotypicFeature . + owl:someValuesFrom biolink:NamedThing . [] a owl:Restriction ; - rdfs:subClassOf biolink:Activity ; + rdfs:subClassOf biolink:StudyPopulation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Activity . + owl:someValuesFrom biolink:StudyPopulation . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:id ], - [ a owl:Restriction ; - owl:allValuesFrom xsd:string ; - owl:onProperty biolink:id ], + owl:minCardinality 1 ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:id ] ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:OntologyClass . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:BioticExposure ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BioticExposure . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Gene ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Gene . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:PhysicalEssence . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ChemicalOrDrugOrTreatment . - -[] a owl:Restriction ; - rdfs:subClassOf [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:allValuesFrom biolink:NamedThing ; - owl:onProperty biolink:object ], + owl:allValuesFrom biolink:Genotype ; + owl:onProperty biolink:subject ], [ a owl:Restriction ; owl:maxCardinality 1 ; owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:maxCardinality 1 ; - owl:onProperty biolink:subject ], + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:subject ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:subject ], [ a owl:Restriction ; - owl:minCardinality 1 ; + owl:maxCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:allValuesFrom xsd:string ; - owl:onProperty biolink:predicate ], - [ a owl:Restriction ; - owl:minCardinality 1 ; owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:ModelToDiseaseAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Behavior ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Behavior . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:NucleicAcidEntity ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:NucleicAcidEntity . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:RelativeFrequencyAnalysisResult ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:RelativeFrequencyAnalysisResult . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:IndividualOrganism ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:IndividualOrganism . + owl:someValuesFrom biolink:GenotypeToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:ClinicalCourse ; + rdfs:subClassOf biolink:AccessibleDnaRegion ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ClinicalCourse . + owl:someValuesFrom biolink:AccessibleDnaRegion . [] a owl:Restriction ; rdfs:subClassOf biolink:ClinicalFinding ; @@ -14494,144 +14492,146 @@ biolink:subject a owl:ObjectProperty ; owl:someValuesFrom biolink:ChemicalMixture . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation ; + rdfs:subClassOf biolink:ReagentTargetedGene ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . + owl:someValuesFrom biolink:ReagentTargetedGene . [] a owl:Restriction ; - rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureToLocationAssociation ; + rdfs:subClassOf biolink:PreprintPublication ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . + owl:someValuesFrom biolink:PreprintPublication . [] a owl:Restriction ; - rdfs:subClassOf biolink:PlanetaryEntity ; + rdfs:subClassOf biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PlanetaryEntity . + owl:someValuesFrom biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Onset ; + rdfs:subClassOf biolink:ComplexChemicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Onset . + owl:someValuesFrom biolink:ComplexChemicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:Study ; + rdfs:subClassOf biolink:SequenceAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Study . + owl:someValuesFrom biolink:SequenceAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:Food ; + rdfs:subClassOf biolink:PairwiseGeneToGeneInteraction ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Food . - -[] a owl:Restriction ; - owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:SubjectOfInvestigation . + owl:someValuesFrom biolink:PairwiseGeneToGeneInteraction . [] a owl:Restriction ; rdfs:subClassOf [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:predicate ], + [ a owl:Restriction ; owl:minCardinality 1 ; - owl:onProperty biolink:object ], + owl:onProperty biolink:predicate ], [ a owl:Restriction ; - owl:allValuesFrom biolink:Disease ; + owl:maxCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:minCardinality 1 ; owl:onProperty biolink:object ], [ a owl:Restriction ; owl:maxCardinality 1 ; - owl:onProperty biolink:object ] ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:minCardinality 1 ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:ChemicalEntityOrGeneOrGeneProduct ; + owl:onProperty biolink:subject ], + [ a owl:Restriction ; + owl:allValuesFrom biolink:NamedThing ; + owl:onProperty biolink:object ], + [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:predicate ] ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:EntityToDiseaseAssociationMixin . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalToChemicalAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalToChemicalAssociation . + owl:someValuesFrom biolink:ChemicalToEntityAssociationMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Event ; + rdfs:subClassOf biolink:PathologicalAnatomicalExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Event . + owl:someValuesFrom biolink:PathologicalAnatomicalExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:VariantToPopulationAssociation ; + rdfs:subClassOf biolink:SmallMolecule ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:VariantToPopulationAssociation . + owl:someValuesFrom biolink:SmallMolecule . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToGeneProductRelationship ; + rdfs:subClassOf biolink:MolecularActivityToMolecularActivityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToGeneProductRelationship . + owl:someValuesFrom biolink:MolecularActivityToMolecularActivityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:CellLine ; + rdfs:subClassOf biolink:EntityToDiseaseAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CellLine . + owl:someValuesFrom biolink:EntityToDiseaseAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:PathologicalProcessExposure ; + rdfs:subClassOf biolink:DiseaseOrPhenotypicFeatureExposure ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:PathologicalProcessExposure . + owl:someValuesFrom biolink:DiseaseOrPhenotypicFeatureExposure . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneToDiseaseAssociation ; + rdfs:subClassOf biolink:GeographicLocationAtTime ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneToDiseaseAssociation . + owl:someValuesFrom biolink:GeographicLocationAtTime . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeneAffectsChemicalAssociation ; + rdfs:subClassOf biolink:MolecularActivityToChemicalEntityAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeneAffectsChemicalAssociation . + owl:someValuesFrom biolink:MolecularActivityToChemicalEntityAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:GeographicExposure ; + rdfs:subClassOf biolink:Genome ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GeographicExposure . + owl:someValuesFrom biolink:Genome . [] a owl:Restriction ; - rdfs:subClassOf biolink:CausalGeneToDiseaseAssociation ; + rdfs:subClassOf biolink:EnvironmentalFeature ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CausalGeneToDiseaseAssociation . + owl:someValuesFrom biolink:EnvironmentalFeature . [] a owl:Restriction ; owl:onProperty linkml:mixins ; - owl:someValuesFrom biolink:GeneOrGeneProduct . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Device ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Device . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:Patent ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Patent . - -[] a owl:Restriction ; - rdfs:subClassOf biolink:ConceptCountAnalysisResult ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ConceptCountAnalysisResult . + owl:someValuesFrom biolink:RelationshipQuantifier . [] a owl:Restriction ; - rdfs:subClassOf biolink:BiologicalProcess ; + rdfs:subClassOf biolink:BookChapter ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:BiologicalProcess . + owl:someValuesFrom biolink:BookChapter . [] a owl:Restriction ; - rdfs:subClassOf biolink:GenotypeToGeneAssociation ; + rdfs:subClassOf biolink:ReactionToCatalystAssociation ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:GenotypeToGeneAssociation . + owl:someValuesFrom biolink:ReactionToCatalystAssociation . [] a owl:Restriction ; - rdfs:subClassOf biolink:ChemicalGeneInteractionAssociation ; + rdfs:subClassOf biolink:OrganismTaxonToOrganismTaxonSpecialization ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:ChemicalGeneInteractionAssociation . + owl:someValuesFrom biolink:OrganismTaxonToOrganismTaxonSpecialization . [] a owl:Restriction ; - rdfs:subClassOf biolink:CorrelatedGeneToDiseaseAssociation ; - owl:onProperty biolink:category ; - owl:someValuesFrom biolink:CorrelatedGeneToDiseaseAssociation . + rdfs:subClassOf [ a owl:Restriction ; + owl:allValuesFrom xsd:string ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:maxCardinality 1 ; + owl:onProperty biolink:name ], + [ a owl:Restriction ; + owl:minCardinality 0 ; + owl:onProperty biolink:name ] ; + owl:onProperty linkml:mixins ; + owl:someValuesFrom biolink:MacromolecularMachineMixin . [] a owl:Restriction ; - rdfs:subClassOf biolink:Haplotype ; + rdfs:subClassOf biolink:ClinicalCourse ; owl:onProperty biolink:category ; - owl:someValuesFrom biolink:Haplotype . + owl:someValuesFrom biolink:ClinicalCourse . diff --git a/project/prefixmap/biolink-model-prefix-map.json b/project/prefixmap/biolink-model-prefix-map.json index ac9ca3db3..2623bdef4 100644 --- a/project/prefixmap/biolink-model-prefix-map.json +++ b/project/prefixmap/biolink-model-prefix-map.json @@ -82,7 +82,6 @@ "HsapDv": "http://purl.obolibrary.org/obo/HsapDv_", "IAO": "http://purl.obolibrary.org/obo/IAO_", "ICD10": "https://icd.who.int/browse10/2016/en#/", - "ICD11": "http://id.who.int/icd/entity/", "ICD9": "http://translator.ncats.nih.gov/ICD9_", "IDO": "http://purl.obolibrary.org/obo/IDO_", "INCHI": "http://identifiers.org/inchi/", diff --git a/project/prefixmap/preferred_prefixes_per_class.json b/project/prefixmap/preferred_prefixes_per_class.json index 98a88e558..737607eea 100644 --- a/project/prefixmap/preferred_prefixes_per_class.json +++ b/project/prefixmap/preferred_prefixes_per_class.json @@ -2064,7 +2064,7 @@ "order": 12 }, { - "prefix": "ICD11", + "prefix": "icd11", "base_uri": "http://id.who.int/icd/entity/", "order": 13 }, diff --git a/project/shacl/biolink_model.shacl.ttl b/project/shacl/biolink_model.shacl.ttl index 8b1ba2960..0a9deeac2 100644 --- a/project/shacl/biolink_model.shacl.ttl +++ b/project/shacl/biolink_model.shacl.ttl @@ -11,44 +11,29 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:description "A region (or regions) of a chromatinized genome that has been measured to be more accessible to an enzyme such as DNase-I or Tn5 Transpose" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; @@ -56,21 +41,27 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:order 0 ; sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:order 1 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -82,29 +73,50 @@ biolink:AccessibleDnaRegion a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ] ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:AccessibleDnaRegion . biolink:Activity a sh:NodeShape ; sh:closed true ; sh:description "An activity is something that occurs over a period of time and acts upon or with entities; it may include consuming, processing, transforming, modifying, relocating, using, or generating entities." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:property [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -112,17 +124,28 @@ biolink:Activity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -139,34 +162,11 @@ biolink:Activity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ] ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Activity . biolink:ActivityAndBehavior a sh:NodeShape ; @@ -177,8 +177,19 @@ biolink:ActivityAndBehavior a sh:NodeShape ; biolink:AdministrativeEntity a sh:NodeShape ; sh:closed false ; - sh:ignoredProperties ( rdf:type biolink:address biolink:affiliation ) ; + sh:ignoredProperties ( biolink:address rdf:type biolink:affiliation ) ; sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], @@ -187,11 +198,12 @@ biolink:AdministrativeEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -205,34 +217,22 @@ biolink:AdministrativeEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -240,52 +240,90 @@ biolink:AdministrativeEntity a sh:NodeShape ; sh:order 5 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ] ; + sh:order 2 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:AdministrativeEntity . biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -293,12 +331,11 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -311,30 +348,28 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -342,226 +377,222 @@ biolink:AnatomicalEntityToAnatomicalEntityAssociation a sh:NodeShape ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:order 18 ; + sh:path biolink:object_category ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . + +biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityAssociation . - -biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is ontogenic, i.e. the two entities are related by development. A number of different relationship types can be used to specify the precise nature of the relationship." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the structure at an earlier time" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; @@ -574,79 +605,132 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at an earlier time" ; + sh:description "the structure at a later time" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . + +biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -654,133 +738,160 @@ biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the structure at a later time" ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:knowledge_source ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityOntogenicAssociation . - -biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A relationship between two anatomical entities where the relationship is mereological, i.e the two entities are related by parthood. This includes relationships between cellular components and cells, between cells and tissues, tissues and whole organisms" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:AnatomicalEntity ; - sh:description "the part" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "the whole" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "the part" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; @@ -792,188 +903,141 @@ biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; + sh:path biolink:object_category ] ; + sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . + +biolink:Annotation a sh:NodeShape ; + sh:closed false ; + sh:description "Biolink Model root class for entity annotations." ; + sh:ignoredProperties ( rdf:type biolink:has_unit biolink:has_numeric_value ) ; + sh:targetClass biolink:Annotation . + +biolink:Article a sh:NodeShape ; + sh:closed true ; + sh:description "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 16 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "the whole" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path biolink:pages ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 2 ; + sh:path biolink:volume ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 1 ; + sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:AnatomicalEntityToAnatomicalEntityPartOfAssociation . - -biolink:Annotation a sh:NodeShape ; - sh:closed false ; - sh:description "Biolink Model root class for entity annotations." ; - sh:ignoredProperties ( biolink:has_unit rdf:type biolink:has_numeric_value ) ; - sh:targetClass biolink:Annotation . - -biolink:Article a sh:NodeShape ; - sh:closed true ; - sh:description "a piece of writing on a particular topic presented as a stand-alone section of a larger publication" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:format ], + sh:order 6 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:rights ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], + sh:order 24 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; - sh:maxCount 1 ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], + sh:order 10 ; + sh:path dct:type ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -986,32 +1050,12 @@ biolink:Article a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:published_in ], - [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:keywords ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_attribute ], + sh:order 25 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; @@ -1019,82 +1063,134 @@ biolink:Article a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:id ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path dct:type ], + sh:order 3 ; + sh:path biolink:issue ], [ sh:datatype xsd:anyURI ; sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:full_name ], + sh:order 21 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:summary ], + sh:order 13 ; + sh:path biolink:format ] ; + sh:targetClass biolink:Article . + +biolink:Association a sh:NodeShape ; + sh:closed true ; + sh:description "A typed association between two entities, supported by evidence" ; + sh:ignoredProperties ( biolink:anatomical_context_qualifier biolink:stage_qualifier biolink:max_research_phase biolink:expression_site biolink:population_context_qualifier biolink:disease_context_qualifier biolink:subject_context_qualifier rdf:type biolink:object_context_qualifier biolink:causal_mechanism_qualifier biolink:reaction_direction biolink:start_interbase_coordinate biolink:stoichiometry biolink:subject_specialization_qualifier biolink:genome_build biolink:quantifier_qualifier biolink:object_aspect_qualifier biolink:has_total biolink:subject_part_qualifier biolink:has_count biolink:clinical_approval_status biolink:onset_qualifier biolink:subject_derivative_qualifier biolink:strand biolink:object_part_qualifier biolink:frequency_qualifier biolink:object_direction_qualifier biolink:phase biolink:species_context_qualifier biolink:catalyst_qualifier biolink:object_form_or_variant_qualifier biolink:object_derivative_qualifier biolink:subject_aspect_qualifier biolink:has_percentage biolink:qualified_predicate biolink:associated_environmental_context biolink:reaction_side biolink:object_specialization_qualifier biolink:FDA_adverse_event_level biolink:end_interbase_coordinate biolink:subject_direction_qualifier biolink:interacting_molecules_category biolink:subject_form_or_variant_qualifier biolink:sex_qualifier biolink:temporal_context_qualifier biolink:has_quotient biolink:phenotypic_state ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:pages ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:deprecated ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:issue ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:license ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:volume ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:creation_date ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:Article . - -biolink:Association a sh:NodeShape ; - sh:closed true ; - sh:description "A typed association between two entities, supported by evidence" ; - sh:ignoredProperties ( biolink:object_part_qualifier biolink:has_total biolink:stage_qualifier biolink:stoichiometry biolink:phenotypic_state biolink:subject_part_qualifier biolink:FDA_adverse_event_level biolink:max_research_phase biolink:subject_context_qualifier biolink:object_context_qualifier biolink:disease_context_qualifier biolink:object_specialization_qualifier biolink:end_interbase_coordinate biolink:phase biolink:population_context_qualifier biolink:expression_site biolink:subject_aspect_qualifier biolink:object_derivative_qualifier biolink:frequency_qualifier biolink:quantifier_qualifier biolink:interacting_molecules_category biolink:subject_specialization_qualifier biolink:start_interbase_coordinate biolink:subject_derivative_qualifier biolink:object_direction_qualifier biolink:has_quotient biolink:sex_qualifier biolink:reaction_direction biolink:object_form_or_variant_qualifier biolink:has_count biolink:qualified_predicate biolink:anatomical_context_qualifier biolink:associated_environmental_context biolink:reaction_side biolink:strand biolink:clinical_approval_status biolink:subject_form_or_variant_qualifier biolink:has_percentage biolink:genome_build rdf:type biolink:catalyst_qualifier biolink:onset_qualifier biolink:causal_mechanism_qualifier biolink:object_aspect_qualifier biolink:species_context_qualifier biolink:temporal_context_qualifier biolink:subject_direction_qualifier ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; @@ -1105,41 +1201,53 @@ biolink:Association a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -1147,87 +1255,56 @@ biolink:Association a sh:NodeShape ; sh:order 14 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -1239,163 +1316,86 @@ biolink:Association a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:path biolink:original_object ] ; + sh:targetClass biolink:Association . + +biolink:Bacterium a sh:NodeShape ; + sh:closed true ; + sh:description "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; + sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Association . - -biolink:Bacterium a sh:NodeShape ; - sh:closed true ; - sh:description "A member of a group of unicellular microorganisms lacking a nuclear membrane, that reproduce by binary fission and are often motile." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; @@ -1408,44 +1408,77 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:description "An association between an mixture behavior and a behavioral feature manifested by the individual exhibited or has exhibited the behavior." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -1457,114 +1490,120 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:order 37 ; + sh:path dct:description ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 41 ; + sh:path biolink:has_total ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 49 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 35 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 40 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:class biolink:BehavioralFeature ; + sh:description "behavioral feature that is the object of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; @@ -1581,143 +1620,108 @@ biolink:BehaviorToBehavioralFeatureAssociation a sh:NodeShape ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_count ], + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_total ], + sh:order 48 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:class biolink:Behavior ; + sh:description "behavior that is the subject of the association" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_quotient ], + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 50 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Behavior ; - sh:description "behavior that is the subject of the association" ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:BehavioralFeature ; - sh:description "behavioral feature that is the object of the association" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ] ; + sh:order 43 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ] ; sh:targetClass biolink:BehaviorToBehavioralFeatureAssociation . biolink:BehavioralExposure a sh:NodeShape ; sh:closed true ; sh:description "A behavioral exposure is a factor relating to behavior impacting an individual." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -1725,55 +1729,39 @@ biolink:BehavioralExposure a sh:NodeShape ; sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path rdfs:label ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -1781,21 +1769,33 @@ biolink:BehavioralExposure a sh:NodeShape ; sh:order 9 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:iri ] ; sh:targetClass biolink:BehavioralExposure . biolink:BehavioralOutcome a sh:NodeShape ; @@ -1806,8 +1806,28 @@ biolink:BehavioralOutcome a sh:NodeShape ; biolink:BiologicalEntity a sh:NodeShape ; sh:closed false ; - sh:ignoredProperties ( biolink:enabled_by biolink:has_zygosity biolink:has_gene_or_gene_product biolink:symbol rdf:type biolink:has_gene biolink:has_output biolink:has_input biolink:has_biological_sequence ) ; - sh:property [ sh:datatype xsd:boolean ; + sh:ignoredProperties ( biolink:enabled_by rdf:type biolink:has_biological_sequence biolink:has_zygosity biolink:has_gene biolink:has_input biolink:has_output biolink:has_gene_or_gene_product biolink:symbol ) ; + sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -1820,48 +1840,22 @@ biolink:BiologicalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -1869,11 +1863,11 @@ biolink:BiologicalEntity a sh:NodeShape ; sh:order 8 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -1884,7 +1878,13 @@ biolink:BiologicalEntity a sh:NodeShape ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ] ; sh:targetClass biolink:BiologicalEntity . biolink:BiologicalProcessOrActivity a sh:NodeShape ; @@ -1897,54 +1897,43 @@ biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:class biolink:PhysicalEntity ; sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -1961,47 +1950,63 @@ biolink:BiologicalProcessOrActivity a sh:NodeShape ; sh:order 1 ; sh:path biolink:has_output ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], + sh:order 3 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ] ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:BiologicalProcessOrActivity . biolink:BioticExposure a sh:NodeShape ; sh:closed true ; sh:description "An external biotic exposure is an intake of (sometimes pathological) biological organisms (including viruses)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -2009,12 +2014,12 @@ biolink:BioticExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -2024,63 +2029,58 @@ biolink:BioticExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ] ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ] ; sh:targetClass biolink:BioticExposure . biolink:Book a sh:NodeShape ; @@ -2088,60 +2088,31 @@ biolink:Book a sh:NodeShape ; sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "Should generally be set to an ontology class defined term for 'book'." ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 8 ; + sh:path biolink:rights ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "Books should have industry-standard identifier such as from ISBN." ; sh:maxCount 1 ; @@ -2149,6 +2120,18 @@ biolink:Book a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; @@ -2156,119 +2139,107 @@ biolink:Book a sh:NodeShape ; sh:order 2 ; sh:path biolink:summary ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], + sh:order 3 ; + sh:path biolink:keywords ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path dct:type ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], + sh:order 15 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ] ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Book . biolink:BookChapter a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "chapter of a book" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:chapter ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:provided_by ], + sh:order 12 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:iri ], + sh:order 21 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "chapter of a book" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:chapter ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:type ], - [ sh:datatype xsd:anyURI ; - sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:published_in ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; @@ -2276,26 +2247,38 @@ biolink:BookChapter a sh:NodeShape ; sh:order 5 ; sh:path biolink:summary ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:volume ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:pages ], + sh:order 11 ; + sh:path biolink:rights ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -2306,52 +2289,69 @@ biolink:BookChapter a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:keywords ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:format ], + sh:order 18 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdfs:label ], + sh:order 22 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:volume ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:order 13 ; + sh:path biolink:creation_date ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:authors ], + [ sh:datatype xsd:anyURI ; + sh:description "The enclosing parent book containing the chapter should have industry-standard identifier from ISBN." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:published_in ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:mesh_terms ] ; + sh:order 19 ; + sh:path biolink:category ] ; sh:targetClass biolink:BookChapter . biolink:CaseToEntityAssociationMixin a sh:NodeShape ; @@ -2365,56 +2365,59 @@ biolink:CaseToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:CaseToEntityAssociationMixin . biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a case (e.g. individual patient) and a phenotypic feature in which the individual has or has had the phenotype." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 50 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -2422,85 +2425,125 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:subject_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], + sh:order 41 ; + sh:path biolink:has_total ], [ sh:class biolink:Case ; sh:description "the case (e.g. patient) that has the property" ; sh:maxCount 1 ; @@ -2509,10 +2552,16 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; @@ -2520,66 +2569,46 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 49 ; sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -2587,74 +2616,34 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:qualified_predicate ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 43 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:order 42 ; + sh:path biolink:has_quotient ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -2665,120 +2654,121 @@ biolink:CaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ] ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:CaseToPhenotypicFeatureAssociation . biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_percentage ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_total ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], + sh:order 26 ; + sh:path biolink:subject_namespace ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:order 6 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -2786,248 +2776,261 @@ biolink:CausalGeneToDiseaseAssociation a sh:NodeShape ; sh:order 38 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], + sh:order 43 ; + sh:path biolink:has_total ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:adjusted_p_value ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:order 11 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 34 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], + sh:order 18 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], + sh:order 49 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 50 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is shown to cause the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_count ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:double ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_quotient ], + sh:order 39 ; + sh:path dct:description ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 37 ; + sh:path rdf:type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 45 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is shown to cause the disease." ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ] ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ] ; sh:targetClass biolink:CausalGeneToDiseaseAssociation . biolink:Cell a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -3035,107 +3038,77 @@ biolink:Cell a sh:NodeShape ; sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ] ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:Cell . biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 4 ; + sh:path biolink:subject_specialization_qualifier ], + [ sh:class biolink:CellLine ; + sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], + sh:order 20 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 39 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 18 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 47 ; sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_specialization_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], + sh:order 44 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; @@ -3143,65 +3116,80 @@ biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 3 ; sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], + sh:order 36 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], + sh:order 48 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], + sh:order 35 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -3209,314 +3197,382 @@ biolink:CellLineAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:subject_specialization_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], + sh:order 17 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:order 5 ; + sh:path biolink:object_specialization_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 16 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:order 6 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:order 45 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 42 ; + sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:CellLine ; - sh:description "A cell line derived from an organismal entity with a disease state that is used as a model of that disease." ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 15 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 38 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], + sh:order 43 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 44 ; - sh:path biolink:subject_direction_qualifier ] ; + sh:order 46 ; + sh:path biolink:object_direction_qualifier ] ; sh:targetClass biolink:CellLineAsAModelOfDiseaseAssociation . biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "An relationship between a cell line and a disease or a phenotype, where the cell line is derived from an individual with that disease or phenotype." ; - sh:ignoredProperties ( biolink:object_direction_qualifier biolink:subject_aspect_qualifier biolink:frequency_qualifier biolink:qualified_predicate rdf:type biolink:object_aspect_qualifier biolink:subject_direction_qualifier ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:ignoredProperties ( biolink:subject_aspect_qualifier rdf:type biolink:qualified_predicate biolink:subject_direction_qualifier biolink:frequency_qualifier biolink:object_direction_qualifier biolink:object_aspect_qualifier ) ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 38 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:subject_specialization_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], + sh:order 18 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:object_specialization_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:original_object ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 3 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 35 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path biolink:category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 29 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 36 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:disease_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_specialization_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:anatomical_context_qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; @@ -3527,81 +3583,32 @@ biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ] ; + sh:order 40 ; + sh:path dct:description ] ; sh:targetClass biolink:CellLineToDiseaseOrPhenotypicFeatureAssociation . biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An relationship between a cell line and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; @@ -3614,98 +3621,91 @@ biolink:CellLineToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:subject ] ; sh:targetClass biolink:CellLineToEntityAssociationMixin . biolink:CellularOrganism a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:property [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + sh:order 6 ; + sh:path biolink:id ] ; sh:targetClass biolink:CellularOrganism . biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; @@ -3713,90 +3713,81 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:description "Describes an effect that a chemical has on a gene or gene product (e.g. an impact of on its abundance, activity,localization, processing, expression, etc.)" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:original_subject ], + sh:order 19 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 53 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 36 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:original_object ], + sh:order 48 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:object_closure ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:causal_mechanism_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 52 ; sh:path biolink:has_attribute ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:object_part_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 50 ; sh:path rdfs:label ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 26 ; - sh:path biolink:knowledge_level ], + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -3804,33 +3795,6 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 46 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:agent_type ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:retrieval_source_ids ], [ sh:class biolink:ChemicalEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -3838,147 +3802,136 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path rdf:subject ], - [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 36 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:qualifiers ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:AnatomicalEntity ; + sh:order 14 ; + sh:path biolink:species_context_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 22 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 53 ; - sh:path biolink:deprecated ], + sh:order 29 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:primary_knowledge_source ], + sh:order 31 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:object_category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:species_context_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:knowledge_source ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 13 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 45 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 7 ; + sh:path biolink:object_part_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:subject_namespace ], + sh:order 44 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:object_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 26 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:adjusted_p_value ], + sh:order 43 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 51 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:has_evidence ], + sh:order 37 ; + sh:path biolink:object_category_closure ], [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_part_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_label_closure ], + sh:order 47 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:negated ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -3986,224 +3939,197 @@ biolink:ChemicalAffectsGeneAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 17 ; sh:path rdf:object ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:iri ], [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:subject_context_qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 45 ; - sh:path biolink:has_supporting_studies ] ; - sh:targetClass biolink:ChemicalAffectsGeneAssociation . - -biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 20 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 25 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 9 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 34 ; + sh:order 49 ; sh:path rdf:type ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 38 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:timepoint ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ] ; + sh:targetClass biolink:ChemicalAffectsGeneAssociation . + +biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -4211,213 +4137,170 @@ biolink:ChemicalEntityAssessesNamedThingAssociation a sh:NodeShape ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . - -biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A regulatory relationship between two genes" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:object_direction_qualifier ], + sh:order 36 ; + sh:path dct:description ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; + sh:order 11 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:qualifier ], + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; + sh:order 31 ; sh:path biolink:id ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:GeneOrGeneProduct ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:negated ], + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], + sh:path biolink:has_supporting_studies ] ; + sh:targetClass biolink:ChemicalEntityAssessesNamedThingAssociation . + +biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A regulatory relationship between two genes" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; @@ -4425,43 +4308,40 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape sh:order 29 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -4469,16 +4349,136 @@ biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation a sh:NodeShape sh:order 14 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "the direction is always from regulator to regulated" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . - -biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; - sh:closed false ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "the direction is always from regulator to regulated" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ] ; + sh:targetClass biolink:ChemicalEntityOrGeneOrGeneProductRegulatesGeneAssociation . + +biolink:ChemicalEntityOrProteinOrPolypeptide a sh:NodeShape ; + sh:closed false ; sh:description "A union of chemical entities and children, and protein and polypeptide. This mixin is helpful to use when searching across chemical entities that must include genes and their children as chemical entities." ; sh:ignoredProperties ( rdf:type ) ; sh:targetClass biolink:ChemicalEntityOrProteinOrPolypeptide . @@ -4494,83 +4494,82 @@ biolink:ChemicalEntityToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; sh:description "the chemical entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; - sh:path rdf:subject ] ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:ChemicalEntityToEntityAssociationMixin . biolink:ChemicalExposure a sh:NodeShape ; sh:closed true ; sh:description "A chemical exposure is an intake of a particular chemical entity." ; sh:ignoredProperties ( biolink:has_gene_or_gene_product rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_attribute_type ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -4578,10 +4577,17 @@ biolink:ChemicalExposure a sh:NodeShape ; sh:order 1 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_attribute_type ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -4589,82 +4595,39 @@ biolink:ChemicalExposure a sh:NodeShape ; sh:order 4 ; sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ] ; + sh:order 7 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:ChemicalExposure . biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:closed true ; sh:description "describes a physical interaction between a chemical entity and a gene or gene product. Any biological or chemical effect resulting from such an interaction are out of scope, and covered by the ChemicalAffectsGeneAssociation type (e.g. impact of a chemical on the abundance, activity, structure, etc, of either participant in the interaction)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; - sh:in ( "metabolite" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 26 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_supporting_studies ], + sh:order 34 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:ChemicalEntity ; sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; @@ -4672,128 +4635,122 @@ biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_namespace ], + sh:order 21 ; + sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:subject_category ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_form_or_variant_qualifier ], + sh:order 5 ; + sh:path biolink:object_part_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:deprecated ], + sh:order 31 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path rdf:type ], + sh:order 43 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:publications ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 45 ; sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 29 ; + sh:path biolink:subject_category_closure ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:in ( "metabolite" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:p_value ], + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:timepoint ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 20 ; - sh:path biolink:agent_type ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_part_qualifier ], + sh:order 44 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_closure ], - [ sh:class biolink:AnatomicalEntity ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path dct:description ], + sh:order 17 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -4802,49 +4759,22 @@ biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:order 10 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:knowledge_source ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 19 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:predicate ], + sh:order 39 ; + sh:path biolink:id ], [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:subject_context_qualifier ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -4857,144 +4787,214 @@ biolink:ChemicalGeneInteractionAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:id ], + sh:order 37 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_label_closure ] ; - sh:targetClass biolink:ChemicalGeneInteractionAssociation . - -biolink:ChemicalMixture a sh:NodeShape ; - sh:closed true ; - sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 18 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:order 33 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 24 ; + sh:path biolink:original_object ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:knowledge_level ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; sh:order 13 ; - sh:path biolink:id ], + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], + sh:order 12 ; + sh:path biolink:qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:AnatomicalEntity ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 46 ; sh:path biolink:deprecated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:provided_by ], + sh:path rdf:predicate ] ; + sh:targetClass biolink:ChemicalGeneInteractionAssociation . + +biolink:ChemicalMixture a sh:NodeShape ; + sh:closed true ; + sh:description "A chemical mixture is a chemical entity composed of two or more molecular entities." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ] ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ChemicalMixture . biolink:ChemicalOrDrugOrTreatment a sh:NodeShape ; @@ -5006,84 +5006,124 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:closed true ; sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disesae or phenotypic feature is a secondary, typically (but not always) undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:qualifier ], + sh:order 45 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 47 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:object_specialization_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 25 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:order 31 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 11 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:primary_knowledge_source ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:subject_specialization_qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:qualifier ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:retrieval_source_ids ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:original_predicate ], + sh:order 8 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -5095,103 +5135,84 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 38 ; + sh:path biolink:p_value ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_specialization_qualifier ], + sh:order 34 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 40 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:p_value ], + sh:order 7 ; + sh:path biolink:FDA_adverse_event_level ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 12 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:anatomical_context_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 19 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_evidence ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; - sh:maxCount 1 ; - sh:order 7 ; - sh:path biolink:FDA_adverse_event_level ], + sh:order 28 ; + sh:path biolink:object_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 21 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:object_label_closure ], + sh:minCount 1 ; + sh:order 22 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -5199,122 +5220,104 @@ biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation sh:order 24 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:original_object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 9 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:negated ], + sh:order 6 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 32 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + sh:order 33 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:original_object ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 10 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 36 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:publications ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:disease_context_qualifier ], + sh:order 20 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:iri ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 22 ; - sh:path biolink:agent_type ] ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:disease_context_qualifier ] ; sh:targetClass biolink:ChemicalOrDrugOrTreatmentSideEffectDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "This association defines a relationship between a chemical or treatment (or procedure) and a disease or phenotypic feature where the disease or phenotypic feature is a secondary undesirable effect." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:p_value ], [ sh:datatype xsd:anyURI ; sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; @@ -5322,62 +5325,86 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:order 6 ; sh:path biolink:object_specialization_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:original_object ], + sh:order 45 ; + sh:path rdfs:label ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path rdf:type ], + [ sh:description "" ; + sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:FDA_adverse_event_level ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:order 42 ; + sh:path biolink:iri ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:subject_specialization_qualifier ], + sh:order 41 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 29 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:object_category_closure ], + sh:order 38 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_supporting_studies ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -5385,188 +5412,151 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:nodeKind sh:IRI ; sh:order 3 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:primary_knowledge_source ], + sh:order 25 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 47 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path rdfs:label ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 8 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 9 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:subject_label_closure ], + sh:order 18 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 48 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 7 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 21 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path rdf:type ], + sh:order 26 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path dct:description ], + sh:order 19 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 34 ; + sh:path biolink:object_namespace ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 22 ; sh:path biolink:agent_type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 21 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_closure ], + sh:order 13 ; + sh:path biolink:negated ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:disease_context_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 10 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:negated ], + sh:order 46 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:object_namespace ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:category ], - [ sh:description "" ; - sh:in ( "life_threatening_adverse_event" "serious_adverse_event" "suspected_adverse_reaction" "unexpected_adverse_event" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:FDA_adverse_event_level ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 47 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:subject_specialization_qualifier ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -5574,45 +5564,69 @@ biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation a sh:No sh:order 23 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 36 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:object_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:aggregator_knowledge_source ] ; + sh:order 35 ; + sh:path biolink:subject_label_closure ] ; sh:targetClass biolink:ChemicalOrDrugOrTreatmentToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:closed true ; sh:description "A relationship between two chemical entities. This can encompass actual interactions as well as temporal causal edges, e.g. one chemical converted to another." ; - sh:ignoredProperties ( biolink:reaction_direction biolink:stoichiometry rdf:type biolink:catalyst_qualifier biolink:reaction_side ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:ignoredProperties ( rdf:type biolink:reaction_direction biolink:reaction_side biolink:stoichiometry biolink:catalyst_qualifier ) ; + sh:property [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -5620,29 +5634,19 @@ biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -5650,176 +5654,230 @@ biolink:ChemicalToChemicalAssociation a sh:NodeShape ; sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:knowledge_source ] ; + sh:targetClass biolink:ChemicalToChemicalAssociation . + +biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the downstream chemical entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; + sh:order 26 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ] ; - sh:targetClass biolink:ChemicalToChemicalAssociation . - -biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "A causal relationship between two chemical entities, where the subject represents the upstream entity and the object represents the downstream. For any such association there is an implicit reaction: IF R has-input C1 AND R has-output C2 AND R enabled-by P AND R type Reaction THEN C1 derives-into C2 catalyst qualifier P" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Study ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 31 ; @@ -5830,45 +5888,121 @@ biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the upstream chemical entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:order 32 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -5880,207 +6014,223 @@ biolink:ChemicalToChemicalDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdf:type ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the upstream chemical entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path dct:description ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path biolink:catalyst_qualifier ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], + sh:order 17 ; + sh:path biolink:original_object ] ; + sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . + +biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; + sh:description "the chemical entity or entity that is an interactor" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; + sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:iri ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; sh:order 34 ; - sh:path biolink:category ], + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 20 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; + sh:order 33 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "this connects the derivation edge to the chemical entity that catalyzes the reaction that causes the subject chemical to transform into the object chemical." ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path biolink:catalyst_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; - sh:path biolink:deprecated ], + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the downstream chemical entity" ; + sh:order 40 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "the disease or phenotype that is affected by the chemical" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; + sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; sh:order 8 ; - sh:path biolink:has_evidence ], + sh:path biolink:qualifier ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 17 ; sh:path biolink:timepoint ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ] ; - sh:targetClass biolink:ChemicalToChemicalDerivationAssociation . - -biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a chemical entity and a phenotype or disease, where the presence of the chemical gives rise to or exacerbates the phenotype." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 37 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:subject_specialization_qualifier ], + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:order 5 ; + sh:path biolink:object_specialization_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -6088,218 +6238,68 @@ biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 21 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 35 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:order 4 ; + sh:path biolink:subject_specialization_qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:negated ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "the disease or phenotype that is affected by the chemical" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_specialization_qualifier ], - [ sh:class biolink:ChemicalEntityOrGeneOrGeneProduct ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ] ; + sh:path biolink:object_label_closure ] ; sh:targetClass biolink:ChemicalToDiseaseOrPhenotypicFeatureAssociation . biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; @@ -6313,66 +6313,123 @@ biolink:ChemicalToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:ChemicalToEntityAssociationMixin . biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a chemical entity and a biological process or pathway." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical entity that is affecting the pathway" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that is affected by the chemical" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -6380,73 +6437,62 @@ biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:order 13 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical entity that is affecting the pathway" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -6454,108 +6500,62 @@ biolink:ChemicalToPathwayAssociation a sh:NodeShape ; sh:order 36 ; sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that is affected by the chemical" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ] ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ] ; sh:targetClass biolink:ChemicalToPathwayAssociation . biolink:ChiSquaredAnalysisResult a sh:NodeShape ; @@ -6563,82 +6563,71 @@ biolink:ChiSquaredAnalysisResult a sh:NodeShape ; sh:description "A result of a chi squared analysis." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -6646,27 +6635,34 @@ biolink:ChiSquaredAnalysisResult a sh:NodeShape ; sh:order 6 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ] ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:ChiSquaredAnalysisResult . biolink:ClinicalCourse a sh:NodeShape ; sh:closed true ; sh:description "The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -6674,34 +6670,12 @@ biolink:ClinicalCourse a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -6709,38 +6683,64 @@ biolink:ClinicalCourse a sh:NodeShape ; sh:order 10 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ] ; sh:targetClass biolink:ClinicalCourse . biolink:ClinicalEntity a sh:NodeShape ; @@ -6748,72 +6748,72 @@ biolink:ClinicalEntity a sh:NodeShape ; sh:description "Any entity or process that exists in the clinical domain and outside the biological realm. Diseases are placed under biological entities" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ] ; + sh:order 7 ; + sh:path rdf:type ] ; sh:targetClass biolink:ClinicalEntity . biolink:ClinicalFinding a sh:NodeShape ; @@ -6821,93 +6821,132 @@ biolink:ClinicalFinding a sh:NodeShape ; sh:description "this category is currently considered broad enough to tag clinical lab measurements and other biological attributes taken as 'clinical traits' with some statistical score, for example, a p value in genetic associations." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 3 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:ClinicalAttribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ] ; + sh:targetClass biolink:ClinicalFinding . + +biolink:ClinicalIntervention a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 5 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 8 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ] ; - sh:targetClass biolink:ClinicalFinding . - -biolink:ClinicalIntervention a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -6915,106 +6954,95 @@ biolink:ClinicalIntervention a sh:NodeShape ; sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:ClinicalIntervention . + +biolink:ClinicalMeasurement a sh:NodeShape ; + sh:closed true ; + sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 10 ; + sh:order 13 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path rdfs:label ], + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 11 ; sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 1 ; + sh:order 7 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ] ; - sh:targetClass biolink:ClinicalIntervention . - -biolink:ClinicalMeasurement a sh:NodeShape ; - sh:closed true ; - sh:description "A clinical measurement is a special kind of attribute which results from a laboratory observation from a subject individual or sample. Measurements can be connected to their subject by the 'has attribute' slot." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -7022,62 +7050,59 @@ biolink:ClinicalMeasurement a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:ClinicalMeasurement . biolink:ClinicalModifier a sh:NodeShape ; sh:closed true ; sh:description "Used to characterize and specify the phenotypic abnormalities defined in the phenotypic abnormality sub-ontology, with respect to severity, laterality, and other aspects" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -7091,107 +7116,86 @@ biolink:ClinicalModifier a sh:NodeShape ; sh:order 8 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ] ; + sh:path biolink:synonym ] ; sh:targetClass biolink:ClinicalModifier . biolink:ClinicalTrial a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; @@ -7203,138 +7207,128 @@ biolink:ClinicalTrial a sh:NodeShape ; sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ] ; + sh:order 6 ; + sh:path biolink:category ] ; sh:targetClass biolink:ClinicalTrial . biolink:CodingSequence a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ] ; + sh:order 14 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:CodingSequence . biolink:Cohort a sh:NodeShape ; sh:closed true ; sh:description "A group of people banded together or treated as a group who share common characteristics. A cohort 'study' is a particular form of longitudinal study that samples a cohort, performing a cross-section at intervals through time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -7342,29 +7336,17 @@ biolink:Cohort a sh:NodeShape ; sh:order 4 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -7377,22 +7359,40 @@ biolink:Cohort a sh:NodeShape ; sh:order 11 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; @@ -7408,6 +7408,11 @@ biolink:CommonDataElement a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -7420,37 +7425,6 @@ biolink:CommonDataElement a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -7463,74 +7437,105 @@ biolink:CommonDataElement a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:creation_date ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:CommonDataElement . biolink:ComplexChemicalExposure a sh:NodeShape ; sh:closed true ; sh:description "A complex chemical exposure is an intake of a chemical mixture (e.g. gasoline), other than a drug." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -7538,86 +7543,76 @@ biolink:ComplexChemicalExposure a sh:NodeShape ; sh:order 3 ; sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ] ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:ComplexChemicalExposure . biolink:ComplexMolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A complex molecular mixture is a chemical mixture composed of two or more molecular entities with unknown concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -7629,13 +7624,24 @@ biolink:ComplexMolecularMixture a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -7648,12 +7654,10 @@ biolink:ComplexMolecularMixture a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:full_name ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -7666,81 +7670,73 @@ biolink:ComplexMolecularMixture a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:trade_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], + sh:order 13 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:datatype xsd:string ; + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ] ; + sh:order 16 ; + sh:path rdf:type ] ; sh:targetClass biolink:ComplexMolecularMixture . biolink:ConceptCountAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a concept count analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -7751,36 +7747,29 @@ biolink:ConceptCountAnalysisResult a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -7792,10 +7781,21 @@ biolink:ConceptCountAnalysisResult a sh:NodeShape ; sh:order 11 ; sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ] ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:format ] ; sh:targetClass biolink:ConceptCountAnalysisResult . biolink:ConfidenceLevel a sh:NodeShape ; @@ -7810,9 +7810,16 @@ biolink:ConfidenceLevel a sh:NodeShape ; sh:order 8 ; sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -7820,99 +7827,110 @@ biolink:ConfidenceLevel a sh:NodeShape ; sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ] ; sh:targetClass biolink:ConfidenceLevel . biolink:ContributorAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between an entity (such as a publication) and various agents that contribute to its realisation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Agent ; + sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -7926,86 +7944,34 @@ biolink:ContributorAssociation a sh:NodeShape ; sh:order 11 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:InformationContentEntity ; sh:description "information content entity which an agent has helped realise" ; sh:maxCount 1 ; @@ -8013,44 +7979,70 @@ biolink:ContributorAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "this field can be used to annotate special characteristics of an agent relationship, such as the fact that a given author agent of a publication is the 'corresponding author'" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -8058,299 +8050,326 @@ biolink:ContributorAssociation a sh:NodeShape ; sh:order 24 ; sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "generally one of the predicate values 'provider', 'publisher', 'editor' or 'author'" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Agent ; - sh:description "agent helping to realise the given entity (e.g. such as a publication)" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ] ; + sh:order 23 ; + sh:path biolink:subject_namespace ] ; sh:targetClass biolink:ContributorAssociation . biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_count ], + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], + sh:order 31 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], + sh:order 28 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_percentage ], + sh:order 44 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 49 ; + sh:path biolink:disease_context_qualifier ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:order 19 ; + sh:path biolink:original_object ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 45 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 42 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:order 41 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 29 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:id ], + sh:order 35 ; + sh:path biolink:iri ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 33 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 32 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is shown to correlate with the disease." ; sh:maxCount 1 ; @@ -8359,62 +8378,43 @@ biolink:CorrelatedGeneToDiseaseAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:order 24 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], + sh:order 38 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], + sh:order 27 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ] ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ] ; sh:targetClass biolink:CorrelatedGeneToDiseaseAssociation . biolink:DatasetSummary a sh:NodeShape ; @@ -8422,70 +8422,38 @@ biolink:DatasetSummary a sh:NodeShape ; sh:description "an item that holds summary level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 0 ; + sh:path biolink:source_web_page ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:format ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], + sh:order 14 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:format ], + sh:order 10 ; + sh:path biolink:id ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -8493,43 +8461,97 @@ biolink:DatasetSummary a sh:NodeShape ; sh:order 5 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path schema1:logo ], + sh:order 11 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:source_web_page ], + sh:order 1 ; + sh:path schema1:logo ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; + sh:order 17 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path biolink:category ] ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path dct:description ] ; sh:targetClass biolink:DatasetSummary . biolink:DatasetVersion a sh:NodeShape ; sh:closed true ; sh:description "an item that holds version level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:rights ], + sh:order 11 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -8542,70 +8564,38 @@ biolink:DatasetVersion a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:deprecated ], - [ sh:class biolink:Dataset ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_dataset ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:ingest_date ], + sh:order 6 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:license ], - [ sh:class biolink:DatasetDistribution ; + sh:order 5 ; + sh:path biolink:format ], + [ sh:class biolink:Dataset ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path dct:distribution ], + sh:order 0 ; + sh:path biolink:has_dataset ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:format ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -8618,71 +8608,72 @@ biolink:DatasetVersion a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ] ; + sh:order 1 ; + sh:path biolink:ingest_date ], + [ sh:class biolink:DatasetDistribution ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path dct:distribution ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:rights ] ; sh:targetClass biolink:DatasetVersion . biolink:DiagnosticAid a sh:NodeShape ; sh:closed true ; sh:description "A device or substance used to help diagnose disease or injury" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -8690,77 +8681,88 @@ biolink:DiagnosticAid a sh:NodeShape ; sh:order 6 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ] ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ] ; sh:targetClass biolink:DiagnosticAid . biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; sh:closed true ; sh:description "A disease or phenotypic feature state, when viewed as an exposure, represents an precondition, leading to or influencing an outcome, e.g. HIV predisposing an individual to infections; a relative deficiency of skin pigmentation predisposing an individual to skin cancer." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 1 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:full_name ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -8768,36 +8770,34 @@ biolink:DiseaseOrPhenotypicFeatureExposure a sh:NodeShape ; sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ] ; + sh:path biolink:has_attribute_type ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureExposure . biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; @@ -8809,13 +8809,13 @@ biolink:DiseaseOrPhenotypicFeatureOutcome a sh:NodeShape ; biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -8823,181 +8823,188 @@ biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToEntityAssociationMixin . biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between either a disease or a phenotypic feature and its mode of (genetic) inheritance." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:GeneticInheritance ; sh:description "genetic inheritance associated with the specified disease or phenotypic feature." ; sh:maxCount 1 ; @@ -9006,247 +9013,234 @@ biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation a sh:NodeShape sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToGeneticInheritanceAssociation . biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between either a disease or a phenotypic feature and an anatomical entity, where the disease/feature manifests in that site." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "anatomical entity in which the disease or feature is found." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -9254,46 +9248,59 @@ biolink:DiseaseOrPhenotypicFeatureToLocationAssociation a sh:NodeShape ; sh:order 29 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "anatomical entity in which the disease or feature is found." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ] ; + sh:order 18 ; + sh:path biolink:object_category ] ; sh:targetClass biolink:DiseaseOrPhenotypicFeatureToLocationAssociation . biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Disease ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Disease ; sh:description "disease class" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -9306,47 +9313,35 @@ biolink:DiseaseToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; + sh:path rdf:predicate ] ; sh:targetClass biolink:DiseaseToEntityAssociationMixin . biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an exposure event and a disease." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -9354,119 +9349,85 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:order 32 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:Disease ; + sh:description "disease class" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:ExposureEvent ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -9474,30 +9435,6 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Disease ; - sh:description "disease class" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; @@ -9510,162 +9447,127 @@ biolink:DiseaseToExposureEventAssociation a sh:NodeShape ; sh:order 14 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:ExposureEvent ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ] ; - sh:targetClass biolink:DiseaseToExposureEventAssociation . - -biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Disease ; - sh:description "disease class" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:p_value ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 36 ; + sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; + sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:double ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_quotient ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:iri ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path rdf:type ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:Onset ; - sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; - sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:onset_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:qualifier ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_namespace ], + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:DiseaseToExposureEventAssociation . + +biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a disease and a phenotypic feature in which the phenotypic feature is associated with the disease in some way." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:sex_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 37 ; + sh:path biolink:id ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; @@ -9673,34 +9575,23 @@ biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 2 ; sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:object_label_closure ], + sh:order 29 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:retrieval_source_ids ], + sh:minCount 1 ; + sh:order 18 ; + sh:path biolink:agent_type ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; @@ -9708,174 +9599,261 @@ biolink:DiseaseToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 30 ; + sh:path biolink:object_namespace ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:knowledge_source ], + sh:order 48 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:negated ], + sh:order 3 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 36 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path rdf:type ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 50 ; sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 48 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:order 1 ; + sh:path biolink:has_count ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:sex_qualifier ], + sh:order 7 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 49 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:id ], + sh:order 34 ; + sh:path biolink:p_value ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path rdf:predicate ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 43 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 18 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path rdfs:label ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 22 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 24 ; + sh:path biolink:object_category ], + [ sh:class biolink:Disease ; + sh:description "disease class" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_count ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:publications ], + sh:order 5 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:deprecated ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 51 ; - sh:path biolink:frequency_qualifier ] ; - sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . - -biolink:DrugExposure a sh:NodeShape ; - sh:closed true ; - sh:description "A drug exposure is an intake of a particular drug." ; - sh:ignoredProperties ( biolink:has_gene_or_gene_product rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; + sh:order 38 ; sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:synonym ], + sh:path biolink:qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdfs:label ], + sh:order 45 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 39 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:negated ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Onset ; + sh:description "a qualifier used in a phenotypic association to state when the phenotype appears is in the subject." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:onset_qualifier ] ; + sh:targetClass biolink:DiseaseToPhenotypicFeatureAssociation . + +biolink:DrugExposure a sh:NodeShape ; + sh:closed true ; + sh:description "A drug exposure is an intake of a particular drug." ; + sh:ignoredProperties ( biolink:has_gene_or_gene_product rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -9888,41 +9866,16 @@ biolink:DrugExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 1 ; sh:path biolink:has_quantitative_value ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -9930,9 +9883,26 @@ biolink:DrugExposure a sh:NodeShape ; sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -9940,136 +9910,166 @@ biolink:DrugExposure a sh:NodeShape ; sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:DrugExposure . - -biolink:DrugLabel a sh:NodeShape ; - sh:closed true ; - sh:description "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 5 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path dct:type ], + sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ] ; + sh:targetClass biolink:DrugExposure . + +biolink:DrugLabel a sh:NodeShape ; + sh:closed true ; + sh:description "a document accompanying a drug or its container that provides written, printed or graphic information about the drug, including drug contents, specific instructions or warnings for administration, storage and disposal instructions, etc." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], + sh:order 18 ; + sh:path rdfs:label ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ], + sh:order 14 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 15 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:format ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + sh:order 11 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:order 3 ; + sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ] ; + sh:order 2 ; + sh:path biolink:summary ] ; sh:targetClass biolink:DrugLabel . biolink:DrugToEntityAssociationMixin a sh:NodeShape ; @@ -10103,53 +10103,17 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "An interaction between a drug and a gene or gene product." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:Drug ; sh:description "the drug that is an interactor" ; sh:maxCount 1 ; @@ -10157,134 +10121,139 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the gene or gene product that is affected by the drug" ; sh:maxCount 1 ; @@ -10292,75 +10261,90 @@ biolink:DrugToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ] ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ] ; sh:targetClass biolink:DrugToGeneAssociation . biolink:DrugToGeneInteractionExposure a sh:NodeShape ; sh:closed true ; sh:description "drug to gene interaction exposure is a drug exposure is where the interactions of the drug with specific genes are known to constitute an 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; @@ -10373,6 +10357,21 @@ biolink:DrugToGeneInteractionExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdf:type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:synonym ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -10380,97 +10379,120 @@ biolink:DrugToGeneInteractionExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_attribute_type ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path biolink:iri ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], [ sh:class biolink:Gene ; sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:has_gene_or_gene_product ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:synonym ] ; + sh:order 14 ; + sh:path dct:description ] ; sh:targetClass biolink:DrugToGeneInteractionExposure . biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 50 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 44 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 45 ; + sh:path biolink:has_percentage ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:object_closure ], [ sh:description "connects an association to an instance of supporting evidence" ; sh:in ( "tclin" "tbio" "tchem" "tdark" ) ; sh:order 10 ; sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; @@ -10478,74 +10500,34 @@ biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:order 14 ; sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 49 ; sh:path biolink:disease_context_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is correlated with the disease in a protective manner, or if the product produced by the gene can be targeted by a small molecule and this leads to a protective or improving disease state." ; sh:maxCount 1 ; @@ -10554,198 +10536,225 @@ biolink:DruggableGeneToDiseaseAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_percentage ], + sh:order 8 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:object_category ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_predicate ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:p_value ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_total ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_count ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path rdfs:label ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:category ], + sh:order 37 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:double ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_quotient ], + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 22 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ] ; + sh:order 20 ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:DruggableGeneToDiseaseAssociation . biolink:Entity a sh:NodeShape ; sh:closed false ; sh:description "Root Biolink Model class for all things and informational relationships, real or imagined." ; - sh:ignoredProperties ( biolink:stoichiometry biolink:phenotypic_state biolink:subject_part_qualifier biolink:knowledge_source biolink:latitude biolink:object_context_qualifier biolink:end_interbase_coordinate dct:distribution biolink:phase biolink:symbol biolink:population_context_qualifier biolink:expression_site biolink:subject_aspect_qualifier biolink:subject_namespace biolink:longitude biolink:mesh_terms biolink:quantifier_qualifier biolink:resource_id biolink:xref biolink:has_quotient biolink:sex_qualifier biolink:has_attribute_type biolink:has_chemical_role biolink:qualified_predicate biolink:object_category_closure biolink:reaction_side biolink:has_procedure biolink:has_taxonomic_rank biolink:has_device biolink:has_gene_or_gene_product biolink:publications biolink:ingest_date biolink:has_quantitative_value biolink:causal_mechanism_qualifier biolink:has_output biolink:chapter biolink:qualifiers biolink:summary biolink:original_subject biolink:negated biolink:object_part_qualifier biolink:drug_regulatory_status_world_wide biolink:is_toxic biolink:format rdf:predicate biolink:creation_date biolink:aggregator_knowledge_source biolink:disease_context_qualifier biolink:primary_knowledge_source biolink:frequency_qualifier biolink:distribution_download_url biolink:in_taxon_label biolink:start_interbase_coordinate biolink:subject_derivative_qualifier biolink:object_direction_qualifier biolink:object_closure biolink:trade_name biolink:has_count biolink:highest_FDA_approval_status biolink:strand biolink:subject_form_or_variant_qualifier biolink:has_percentage biolink:p_value biolink:qualifier biolink:agent_type biolink:object_aspect_qualifier biolink:pages biolink:subject_direction_qualifier biolink:has_supporting_studies biolink:upstream_resource_ids biolink:has_qualitative_value biolink:stage_qualifier biolink:is_metabolite biolink:FDA_adverse_event_level biolink:has_gene biolink:max_research_phase biolink:subject_context_qualifier biolink:enabled_by biolink:object_specialization_qualifier biolink:is_supplement biolink:full_name biolink:source_web_page biolink:has_drug biolink:object_derivative_qualifier biolink:original_object biolink:interacting_molecules_category biolink:subject_specialization_qualifier biolink:has_evidence biolink:has_zygosity biolink:routes_of_delivery biolink:reaction_direction biolink:retrieval_source_ids biolink:object_form_or_variant_qualifier biolink:associated_environmental_context biolink:published_in schema1:logo biolink:object_namespace biolink:synonym biolink:has_biological_sequence biolink:keywords biolink:clinical_approval_status biolink:object_label_closure biolink:iso_abbreviation biolink:has_dataset biolink:subject_closure biolink:catalyst_qualifier biolink:onset_qualifier rdf:object biolink:provided_by biolink:knowledge_level biolink:issue dct:type biolink:timepoint biolink:license biolink:has_total rdf:subject biolink:subject_label_closure biolink:object_category biolink:max_tolerated_dose biolink:resource_role biolink:authors biolink:available_from biolink:anatomical_context_qualifier biolink:subject_category biolink:affiliation biolink:in_taxon biolink:subject_category_closure biolink:adjusted_p_value biolink:volume biolink:rights biolink:genome_build rdf:type biolink:address biolink:species_context_qualifier biolink:has_input biolink:temporal_context_qualifier biolink:original_predicate ) ; - sh:property [ sh:class biolink:Attribute ; + sh:ignoredProperties ( biolink:original_subject biolink:has_quantitative_value biolink:chapter biolink:latitude biolink:has_input biolink:summary biolink:has_gene_or_gene_product biolink:ingest_date dct:distribution biolink:subject_context_qualifier biolink:enabled_by biolink:has_procedure biolink:reaction_direction biolink:volume biolink:adjusted_p_value biolink:has_dataset biolink:has_gene biolink:object_category biolink:clinical_approval_status biolink:has_qualitative_value biolink:has_device biolink:subject_label_closure biolink:object_part_qualifier biolink:affiliation biolink:has_output biolink:original_object biolink:catalyst_qualifier biolink:subject_category biolink:timepoint biolink:has_chemical_role biolink:subject_aspect_qualifier biolink:has_percentage biolink:qualified_predicate biolink:subject_direction_qualifier biolink:negated biolink:resource_role biolink:sex_qualifier biolink:temporal_context_qualifier biolink:has_attribute_type biolink:has_biological_sequence biolink:max_research_phase biolink:population_context_qualifier biolink:address biolink:rights biolink:stoichiometry biolink:trade_name biolink:mesh_terms biolink:creation_date biolink:license biolink:is_metabolite biolink:subject_category_closure biolink:knowledge_source biolink:xref biolink:phase biolink:published_in biolink:symbol biolink:knowledge_level biolink:object_specialization_qualifier biolink:FDA_adverse_event_level biolink:interacting_molecules_category biolink:phenotypic_state biolink:anatomical_context_qualifier rdf:subject biolink:expression_site biolink:source_web_page biolink:object_category_closure biolink:full_name biolink:retrieval_source_ids biolink:has_supporting_studies biolink:subject_closure biolink:routes_of_delivery biolink:object_context_qualifier biolink:causal_mechanism_qualifier biolink:issue biolink:resource_id dct:type biolink:has_zygosity biolink:subject_specialization_qualifier biolink:genome_build biolink:object_aspect_qualifier biolink:aggregator_knowledge_source biolink:has_count rdf:predicate biolink:onset_qualifier biolink:pages biolink:strand schema1:logo biolink:object_form_or_variant_qualifier biolink:in_taxon_label biolink:object_derivative_qualifier biolink:primary_knowledge_source biolink:end_interbase_coordinate biolink:highest_FDA_approval_status biolink:max_tolerated_dose biolink:longitude biolink:synonym biolink:object_closure biolink:authors biolink:drug_regulatory_status_world_wide biolink:is_toxic biolink:has_drug biolink:has_evidence biolink:stage_qualifier biolink:iso_abbreviation biolink:disease_context_qualifier biolink:format biolink:in_taxon rdf:type biolink:upstream_resource_ids biolink:qualifiers rdf:object biolink:start_interbase_coordinate biolink:quantifier_qualifier biolink:provided_by biolink:object_label_closure biolink:subject_part_qualifier biolink:has_total biolink:subject_derivative_qualifier biolink:p_value biolink:is_supplement biolink:subject_namespace biolink:frequency_qualifier biolink:available_from biolink:object_direction_qualifier biolink:species_context_qualifier biolink:object_namespace biolink:publications biolink:agent_type biolink:distribution_download_url biolink:associated_environmental_context biolink:reaction_side biolink:qualifier biolink:subject_form_or_variant_qualifier biolink:has_taxonomic_rank biolink:has_quotient biolink:original_predicate biolink:keywords ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -10759,21 +10768,12 @@ biolink:Entity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path rdfs:label ] ; + sh:order 7 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Entity . biolink:EntityToDiseaseAssociation a sh:NodeShape ; @@ -10784,221 +10784,204 @@ biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 16 ; + sh:path biolink:original_subject ], + [ sh:description "" ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 0 ; + sh:path biolink:clinical_approval_status ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], + sh:order 30 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:max_research_phase ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], + sh:order 33 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], + sh:order 23 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:deprecated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], + sh:order 25 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -11006,34 +10989,58 @@ biolink:EntityToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:subject ], - [ sh:description "" ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ] ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ] ; sh:targetClass biolink:EntityToDiseaseAssociation . biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "mixin class for any association whose object (target node) is a disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:frequency_qualifier ], + sh:order 3 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -11041,25 +11048,12 @@ biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:subject ], [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path rdf:object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:object_direction_qualifier ], + sh:order 5 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; @@ -11067,17 +11061,23 @@ biolink:EntityToDiseaseAssociationMixin a sh:NodeShape ; sh:order 4 ; sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 2 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:disease_context_qualifier ] ; + sh:order 7 ; + sh:path rdf:subject ] ; sh:targetClass biolink:EntityToDiseaseAssociationMixin . biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; @@ -11095,13 +11095,6 @@ biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:anatomical_context_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -11109,12 +11102,19 @@ biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:anyURI ; sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_specialization_qualifier ], + sh:order 4 ; + sh:path biolink:subject_specialization_qualifier ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "disease or phenotype" ; sh:maxCount 1 ; @@ -11126,8 +11126,8 @@ biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:subject_specialization_qualifier ] ; + sh:order 5 ; + sh:path biolink:object_specialization_qualifier ] ; sh:targetClass biolink:EntityToDiseaseOrPhenotypicFeatureAssociationMixin . biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; @@ -11141,26 +11141,26 @@ biolink:EntityToExposureEventAssociationMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ] ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:EntityToExposureEventAssociationMixin . biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifiers for entity to disease or phenotype associations." ; - sh:ignoredProperties ( biolink:has_percentage biolink:has_quotient biolink:has_total biolink:sex_qualifier biolink:has_count rdf:type ) ; + sh:ignoredProperties ( biolink:has_percentage rdf:type biolink:sex_qualifier biolink:has_quotient biolink:has_total biolink:has_count ) ; sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -11169,13 +11169,20 @@ biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:order 7 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdf:predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_direction_qualifier ], @@ -11191,57 +11198,50 @@ biolink:EntityToFeatureOrDiseaseQualifiersMixin a sh:NodeShape ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdf:predicate ] ; + sh:order 6 ; + sh:path biolink:frequency_qualifier ] ; sh:targetClass biolink:EntityToFeatureOrDiseaseQualifiersMixin . biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "An association between some entity and an outcome" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -11254,101 +11254,118 @@ biolink:EntityToOutcomeAssociationMixin a sh:NodeShape ; biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:max_research_phase ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:description "" ; + sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:clinical_approval_status ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 29 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], + sh:order 26 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], + sh:order 24 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 29 ; - sh:path biolink:retrieval_source_ids ], + sh:order 35 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 37 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "" ; - sh:in ( "approved_for_condition" "fda_approved_for_condition" "not_approved_for_condition" "post_approval_withdrawal" "off_label_use" "not_provided" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:clinical_approval_status ], + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], + sh:order 5 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -11356,23 +11373,29 @@ biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 39 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:subject ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; @@ -11380,21 +11403,32 @@ biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 30 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -11402,90 +11436,56 @@ biolink:EntityToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:in ( "pre_clinical_research_phase" "clinical_trial_phase" "clinical_trial_phase_1" "clinical_trial_phase_2" "clinical_trial_phase_3" "clinical_trial_phase_4" "not_provided" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:max_research_phase ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:order 38 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], + sh:order 7 ; + sh:path biolink:qualifiers ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:agent_type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], + sh:order 31 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ] ; + sh:order 17 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociation . biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; @@ -11504,24 +11504,17 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 6 ; + sh:path biolink:has_quotient ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:has_percentage ], + sh:order 4 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; @@ -11547,80 +11540,59 @@ biolink:EntityToPhenotypicFeatureAssociationMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:has_percentage ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 9 ; sh:path biolink:subject_direction_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:double ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:has_quotient ], + sh:order 10 ; + sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:has_count ] ; + sh:path rdf:subject ] ; sh:targetClass biolink:EntityToPhenotypicFeatureAssociationMixin . biolink:EnvironmentalExposure a sh:NodeShape ; sh:closed true ; sh:description "A environmental exposure is a factor relating to abiotic processes in the environment including sunlight (UV-B), atmospheric (heat, cold, general pollution) and water-born contaminants." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; @@ -11628,33 +11600,59 @@ biolink:EnvironmentalExposure a sh:NodeShape ; sh:order 1 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 2 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -11663,33 +11661,34 @@ biolink:EnvironmentalExposure a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:QuantityValue ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_attribute_type ] ; + sh:order 4 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:EnvironmentalExposure . biolink:EnvironmentalFeature a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; @@ -11700,33 +11699,29 @@ biolink:EnvironmentalFeature a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -11734,107 +11729,89 @@ biolink:EnvironmentalFeature a sh:NodeShape ; sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ] ; + sh:order 6 ; + sh:path biolink:category ] ; sh:targetClass biolink:EnvironmentalFeature . biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:trade_name ], + sh:order 3 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:synonym ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:is_toxic ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; @@ -11845,82 +11822,105 @@ biolink:EnvironmentalFoodContaminant a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ] ; - sh:targetClass biolink:EnvironmentalFoodContaminant . - -biolink:EnvironmentalProcess a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 11 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:EnvironmentalFoodContaminant . + +biolink:EnvironmentalProcess a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 2 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 6 ; + sh:path biolink:category ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ] ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ] ; sh:targetClass biolink:EnvironmentalProcess . biolink:EpidemiologicalOutcome a sh:NodeShape ; @@ -11944,60 +11944,61 @@ biolink:Event a sh:NodeShape ; sh:closed true ; sh:description "Something that happens at a given place and time." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -12005,12 +12006,11 @@ biolink:Event a sh:NodeShape ; sh:order 9 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ] ; + sh:order 2 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Event . biolink:ExonToTranscriptRelationship a sh:NodeShape ; @@ -12024,29 +12024,57 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -12054,104 +12082,78 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], [ sh:class biolink:Transcript ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -12159,269 +12161,217 @@ biolink:ExonToTranscriptRelationship a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ] ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ExonToTranscriptRelationship . biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between an exposure event and an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Outcome ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 35 ; + sh:path biolink:category ], + [ sh:datatype xsd:time ; + sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:temporal_context_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:subject_category ], + sh:order 20 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:qualifiers ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], + sh:order 17 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 39 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:agent_type ], + sh:order 0 ; + sh:path biolink:population_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_object ], + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:subject_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a constraint of time placed upon the truth value of an association. for time intervales, use temporal interval qualifier." ; + sh:order 30 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:temporal_context_qualifier ], + sh:order 25 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -12429,58 +12379,108 @@ biolink:ExposureEventToOutcomeAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path rdf:predicate ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:population_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 29 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_predicate ], + sh:order 5 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 39 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_namespace ], + sh:order 12 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Outcome ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:timepoint ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 24 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ] ; + sh:order 33 ; + sh:path biolink:id ] ; sh:targetClass biolink:ExposureEventToOutcomeAssociation . biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; @@ -12488,57 +12488,92 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "Any association between an environment and a phenotypic feature, where being in the environment influences the phenotype." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 46 ; sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 37 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -12546,12 +12581,17 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 40 ; + sh:path biolink:has_count ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -12559,117 +12599,114 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 14 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:order 36 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_count ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 49 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 32 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 43 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 48 ; + sh:path biolink:qualified_predicate ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -12677,17 +12714,12 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], [ sh:class biolink:ExposureEvent ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -12695,114 +12727,88 @@ biolink:ExposureEventToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_quotient ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:has_total ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:frequency_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ] ; + sh:path biolink:subject_category ] ; sh:targetClass biolink:ExposureEventToPhenotypicFeatureAssociation . biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifiers for disease or phenotype to entity associations." ; - sh:ignoredProperties ( biolink:has_percentage biolink:has_quotient biolink:sex_qualifier biolink:has_total biolink:has_count rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:ignoredProperties ( biolink:has_percentage rdf:type biolink:sex_qualifier biolink:has_quotient biolink:has_total biolink:has_count ) ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualified_predicate ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:subject ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -12810,18 +12816,6 @@ biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path rdf:object ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -12834,6 +12828,12 @@ biolink:FeatureOrDiseaseQualifiersToEntityMixin a sh:NodeShape ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:subject_direction_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; @@ -12846,61 +12846,48 @@ biolink:Food a sh:NodeShape ; sh:closed true ; sh:description "A substance consumed by a living organism as a source of nutrition" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:order 7 ; + sh:path biolink:is_toxic ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; sh:order 3 ; sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], + sh:order 14 ; + sh:path biolink:iri ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 16 ; @@ -12911,36 +12898,34 @@ biolink:Food a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path biolink:synonym ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_chemical_role ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -12949,64 +12934,94 @@ biolink:Food a sh:NodeShape ; sh:order 13 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:category ] ; - sh:targetClass biolink:Food . - -biolink:FoodAdditive a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; + sh:order 4 ; sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:highest_FDA_approval_status ] ; + sh:targetClass biolink:Food . + +biolink:FoodAdditive a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:is_toxic ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:has_chemical_role ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -13014,27 +13029,24 @@ biolink:FoodAdditive a sh:NodeShape ; sh:order 16 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:has_chemical_role ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -13042,36 +13054,24 @@ biolink:FoodAdditive a sh:NodeShape ; sh:order 13 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:is_toxic ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ] ; + sh:order 2 ; + sh:path biolink:max_tolerated_dose ] ; sh:targetClass biolink:FoodAdditive . biolink:FrequencyQualifierMixin a sh:NodeShape ; sh:closed false ; sh:description "Qualifier for frequency type associations" ; - sh:ignoredProperties ( biolink:disease_context_qualifier biolink:has_percentage biolink:object_direction_qualifier biolink:has_quotient biolink:has_total biolink:sex_qualifier biolink:subject_aspect_qualifier biolink:has_count biolink:qualified_predicate rdf:type biolink:object_aspect_qualifier biolink:subject_direction_qualifier ) ; - sh:property [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:ignoredProperties ( biolink:subject_aspect_qualifier biolink:has_percentage rdf:type biolink:qualified_predicate biolink:subject_direction_qualifier biolink:object_direction_qualifier biolink:sex_qualifier biolink:disease_context_qualifier biolink:object_aspect_qualifier biolink:has_quotient biolink:has_total biolink:has_count ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; @@ -13079,170 +13079,176 @@ biolink:FrequencyQualifierMixin a sh:NodeShape ; sh:order 0 ; sh:path biolink:frequency_qualifier ], [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 1 ; + sh:path rdf:subject ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ] ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ] ; sh:targetClass biolink:FrequencyQualifierMixin . biolink:FrequencyQuantifier a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:integer ; + sh:property [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_count ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:has_total ] ; + sh:path biolink:has_total ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_quotient ] ; sh:targetClass biolink:FrequencyQuantifier . biolink:FunctionalAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a macromolecular machine mixin (gene, gene product or complex of gene products) and either a molecular activity, a biological process or a cellular location in which a function is executed." ; - sh:ignoredProperties ( biolink:species_context_qualifier rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:ignoredProperties ( rdf:type biolink:species_context_qualifier ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -13250,22 +13256,19 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; @@ -13273,23 +13276,39 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -13297,58 +13316,39 @@ biolink:FunctionalAssociation a sh:NodeShape ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ] ; + sh:order 38 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:FunctionalAssociation . biolink:Fungus a sh:NodeShape ; @@ -13356,43 +13356,55 @@ biolink:Fungus a sh:NodeShape ; sh:description "A kingdom of eukaryotic, heterotrophic organisms that live as saprobes or parasites, including mushrooms, yeasts, smuts, molds, etc. They reproduce either sexually or asexually, and have life cycles that range from simple to complex. Filamentous fungi refer to those that grow as multicellular colonies (mushrooms and molds)." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -13400,199 +13412,167 @@ biolink:Fungus a sh:NodeShape ; sh:order 1 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:Fungus . biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; sh:closed true ; sh:description "Describes an effect that a gene or gene product has on a chemical entity (e.g. an impact of on its abundance, activity, localization, processing, transport, etc.)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; - sh:in ( "metabolite" ) ; + sh:property [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 11 ; - sh:path biolink:object_derivative_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 46 ; - sh:path biolink:has_supporting_studies ], + sh:order 21 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 50 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 54 ; + sh:path biolink:deprecated ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:ChemicalEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 43 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path rdf:object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 15 ; + sh:path biolink:species_context_qualifier ], + [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:adjusted_p_value ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 6 ; + sh:path biolink:object_form_or_variant_qualifier ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 28 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:subject_context_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:order 44 ; + sh:path biolink:p_value ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:subject_derivative_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 5 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; + sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 16 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path biolink:subject_part_qualifier ], + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:object_category ], + sh:order 12 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path rdfs:label ], + sh:order 39 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:iri ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:order 6 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 54 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:subject_category_closure ], + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 53 ; - sh:path biolink:has_attribute ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 25 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 27 ; - sh:path biolink:knowledge_level ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 28 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:subject_derivative_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 45 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:ChemicalEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:p_value ], + sh:order 24 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; @@ -13600,209 +13580,238 @@ biolink:GeneAffectsChemicalAssociation a sh:NodeShape ; sh:order 14 ; sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:object_category_closure ], - [ sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "genetic_variant_form" "modified_form" "loss_of_function_variant_form" "gain_of_function_variant_form" "polymorphic_form" "snp_form" "analog_form" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:publications ], + sh:order 17 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:subject_closure ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 12 ; - sh:path biolink:causal_mechanism_qualifier ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:order 8 ; - sh:path biolink:object_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:original_object ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:object_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:original_subject ], + sh:order 23 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 52 ; sh:path dct:description ], - [ sh:class biolink:AnatomicalEntity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:subject_context_qualifier ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:species_context_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:negated ], + sh:order 41 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:object_label_closure ], + sh:order 47 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 53 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 49 ; + sh:path biolink:category ], + [ sh:class biolink:AnatomicalEntity ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:subject_category ], + sh:order 9 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 51 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:knowledge_source ], + sh:order 29 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:AnatomicalEntity ; sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:anatomical_context_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:subject_category ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 46 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:primary_knowledge_source ], + sh:order 42 ; + sh:path biolink:object_label_closure ], + [ sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; + sh:in ( "metabolite" ) ; + sh:maxCount 1 ; + sh:order 11 ; + sh:path biolink:object_derivative_qualifier ], [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; sh:maxCount 1 ; sh:order 7 ; sh:path biolink:object_part_qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 16 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 43 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:object_closure ], - [ sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; - sh:in ( "3_prime_utr" "5_prime_utr" "polya_tail" "promoter" "enhancer" "exon" "intron" ) ; + sh:order 31 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:subject_part_qualifier ] ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:original_subject ] ; sh:targetClass biolink:GeneAffectsChemicalAssociation . biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path dct:description ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 50 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 49 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:deprecated ], + sh:order 45 ; + sh:path biolink:has_percentage ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -13810,192 +13819,195 @@ biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 38 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 44 ; sh:path biolink:has_quotient ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:category ], + sh:order 34 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 33 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:disease_context_qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], + sh:order 19 ; + sh:path biolink:original_object ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:timepoint ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], + sh:order 48 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:has_total ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 42 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -14003,45 +14015,33 @@ biolink:GeneAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 21 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_percentage ], + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ] ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:GeneAsAModelOfDiseaseAssociation . biolink:GeneExpressionMixin a sh:NodeShape ; @@ -14054,6 +14054,12 @@ biolink:GeneExpressionMixin a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:expression_site ], + [ sh:class biolink:OntologyClass ; + sh:description "Optional quantitative value indicating degree of expression." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; @@ -14065,13 +14071,7 @@ biolink:GeneExpressionMixin a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:stage_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ] ; + sh:path biolink:stage_qualifier ] ; sh:targetClass biolink:GeneExpressionMixin . biolink:GeneGroupingMixin a sh:NodeShape ; @@ -14089,189 +14089,204 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:qualified_predicate ], + sh:order 38 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], + sh:order 17 ; + sh:path biolink:timepoint ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 48 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 43 ; + sh:path biolink:has_count ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 51 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 5 ; sh:path biolink:object_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], + sh:order 49 ; + sh:path biolink:qualified_predicate ], [ sh:class biolink:BiologicalSex ; sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_total ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 16 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 46 ; + sh:path biolink:has_percentage ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:subject_form_or_variant_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "A gene that has a role in modeling the disease. This may be a model organism ortholog of a known disease gene, or it may be a gene whose mutants recapitulate core features of the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 1 ; - sh:path rdf:subject ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 51 ; - sh:path biolink:frequency_qualifier ], + sh:order 40 ; + sh:path dct:description ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 50 ; sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 44 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 19 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:order 26 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -14279,119 +14294,109 @@ biolink:GeneHasVariantThatContributesToDiseaseAssociation a sh:NodeShape ; sh:order 36 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:order 47 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 0 ; + sh:path biolink:subject_form_or_variant_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 18 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], + sh:order 39 ; + sh:path rdfs:label ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:order 35 ; + sh:path biolink:id ], [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; sh:maxCount 1 ; sh:order 4 ; sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ] ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:GeneHasVariantThatContributesToDiseaseAssociation . biolink:GeneProductIsoformMixin a sh:NodeShape ; sh:closed false ; sh:description "This is an abstract class that can be mixed in with different kinds of gene products to indicate that the gene product is intended to represent a specific isoform rather than a canonical or reference or generic product. The designation of canonical or reference may be arbitrary, or it may represent the superclass of all isoforms." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; @@ -14401,12 +14406,7 @@ biolink:GeneProductIsoformMixin a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:GeneProductIsoformMixin . biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; @@ -14414,21 +14414,28 @@ biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; sh:description "Describes a regulatory relationship between two genes or gene products." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -14436,91 +14443,18 @@ biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:species_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -14532,58 +14466,52 @@ biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_closure ], - [ sh:description "the aspect of the object gene or gene product that is being regulated, must be a descendant of \"activity_or_abundance\"\"" ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 0 ; - sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 42 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 1 ; sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -14591,166 +14519,176 @@ biolink:GeneRegulatesGeneAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 6 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:qualified_predicate ], + sh:order 24 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], + sh:order 28 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:GeneRegulatesGeneAssociation . - -biolink:GeneToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type biolink:subject_form_or_variant_qualifier ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 3 ; + sh:path biolink:species_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path dct:description ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; + sh:order 35 ; + sh:path biolink:id ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], + sh:order 17 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:id ], + sh:order 40 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_total ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; + sh:order 39 ; sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], + [ sh:description "the aspect of the object gene or gene product that is being regulated, must be a descendant of \"activity_or_abundance\"\"" ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 0 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:category ], + sh:path biolink:primary_knowledge_source ] ; + sh:targetClass biolink:GeneRegulatesGeneAssociation . + +biolink:GeneToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type biolink:subject_form_or_variant_qualifier ) ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; @@ -14758,246 +14696,236 @@ biolink:GeneToDiseaseAssociation a sh:NodeShape ; sh:order 42 ; sh:path biolink:has_count ], [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:description "disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 18 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 28 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path rdf:type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 32 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], + sh:order 6 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], + sh:order 44 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:order 16 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:order 27 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 39 ; + sh:path dct:description ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the disease, may be protective or causative or associative, or as a model" ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:object_direction_qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:order 26 ; + sh:path biolink:subject_namespace ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:knowledge_level ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ] ; - sh:targetClass biolink:GeneToDiseaseAssociation . - -biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type biolink:subject_form_or_variant_qualifier ) ; - sh:property [ sh:datatype xsd:string ; + [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:disease_context_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path rdfs:label ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene in which variation is correlated with the phenotypic feature" ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:subject ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], + sh:order 50 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -15005,24 +14933,47 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:id ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 49 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:path biolink:qualifier ] ; + sh:targetClass biolink:GeneToDiseaseAssociation . + +biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type biolink:subject_form_or_variant_qualifier ) ; + sh:property [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], + sh:order 50 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:class biolink:DiseaseOrPhenotypicFeature ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -15030,78 +14981,101 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path rdf:object ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:has_percentage ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 0 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:double ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_quotient ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; - sh:maxCount 1 ; + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_count ], + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 11 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ], + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 35 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 41 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -15109,169 +15083,195 @@ biolink:GeneToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 21 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_percentage ], + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 33 ; sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 25 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:category ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_total ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; - sh:maxCount 1 ; - sh:order 0 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], + sh:order 39 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:subject_category ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_total ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 49 ; + sh:path biolink:disease_context_qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene in which variation is correlated with the phenotypic feature" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:order 42 ; + sh:path biolink:has_count ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 24 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ] ; + sh:order 27 ; + sh:path biolink:object_namespace ] ; sh:targetClass biolink:GeneToDiseaseOrPhenotypicFeatureAssociation . biolink:GeneToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:GeneOrGeneProduct ; - sh:description "gene that is the subject of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "gene that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -15285,29 +15285,24 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a gene and a gene expression site, possibly qualified by stage/timing info." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_label_closure ], + sh:order 35 ; + sh:path biolink:category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "expression relationship" ; sh:maxCount 1 ; @@ -15315,12 +15310,12 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:primary_knowledge_source ], + sh:order 5 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -15328,427 +15323,432 @@ biolink:GeneToExpressionSiteAssociation a sh:NodeShape ; sh:order 19 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "Gene or gene product positively within the specified anatomical entity (or subclass, i.e. cellular component) location." ; + sh:order 28 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; - sh:description "can be used to indicate magnitude, or also ranking" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:quantifier_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path dct:description ], + sh:order 23 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:qualifier ], - [ sh:class biolink:LifeStage ; - sh:description "stage at which the gene is expressed in the site" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:stage_qualifier ], + sh:order 33 ; + sh:path biolink:id ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 29 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which the gene is expressed" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:negated ], + sh:order 37 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 26 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:knowledge_source ], + sh:order 40 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path rdf:type ], + [ sh:class biolink:LifeStage ; + sh:description "stage at which the gene is expressed in the site" ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:object_category_closure ], + sh:order 0 ; + sh:path biolink:stage_qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "can be used to indicate magnitude, or also ranking" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:quantifier_qualifier ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which the gene is expressed" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:adjusted_p_value ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 22 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:has_supporting_studies ], + sh:order 20 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:subject_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_evidence ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 14 ; sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 15 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:p_value ], + sh:order 6 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 39 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:object_closure ], + sh:order 10 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 25 ; - sh:path biolink:subject_namespace ] ; - sh:targetClass biolink:GeneToExpressionSiteAssociation . - -biolink:GeneToGeneAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; - sh:ignoredProperties ( biolink:stage_qualifier biolink:expression_site biolink:phenotypic_state rdf:type biolink:quantifier_qualifier biolink:interacting_molecules_category ) ; - sh:property [ sh:datatype xsd:string ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; + sh:order 16 ; sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 27 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 10 ; + sh:order 12 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 11 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; + sh:order 21 ; sh:path biolink:subject_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 31 ; + sh:path biolink:adjusted_p_value ] ; + sh:targetClass biolink:GeneToExpressionSiteAssociation . + +biolink:GeneToGeneAssociation a sh:NodeShape ; + sh:closed false ; + sh:description "abstract parent class for different kinds of gene-gene or gene product to gene product relationships. Includes homology and interaction." ; + sh:ignoredProperties ( rdf:type biolink:stage_qualifier biolink:quantifier_qualifier biolink:interacting_molecules_category biolink:expression_site biolink:phenotypic_state ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; - sh:path biolink:object_category ] ; + sh:path biolink:object_category ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:GeneToGeneAssociation . biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; @@ -15760,64 +15760,33 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 26 ; sh:path biolink:object_category_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 41 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 4 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], - [ sh:class biolink:LifeStage ; - sh:description "stage during which gene or protein expression of takes place." ; - sh:maxCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:stage_qualifier ], + sh:order 9 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ], + sh:order 39 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -15825,52 +15794,64 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path rdf:predicate ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + sh:order 18 ; + sh:path biolink:original_subject ], + [ sh:class biolink:LifeStage ; + sh:description "stage during which gene or protein expression of takes place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:stage_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 21 ; + sh:path biolink:subject_category ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:timepoint ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 4 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], [ sh:class biolink:AnatomicalEntity ; sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; @@ -15878,21 +15859,22 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:order 1 ; sh:path biolink:expression_site ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], + sh:order 20 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; @@ -15905,17 +15887,6 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:minCount 1 ; sh:order 15 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -15923,40 +15894,33 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 6 ; sh:path rdf:object ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:phenotypic_state ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], + sh:order 30 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 34 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -15964,221 +15928,248 @@ biolink:GeneToGeneCoexpressionAssociation a sh:NodeShape ; sh:order 40 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], + sh:order 36 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 41 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:order 12 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ] ; - sh:targetClass biolink:GeneToGeneCoexpressionAssociation . - -biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:time ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; + sh:order 17 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 35 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; + sh:order 24 ; sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 13 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ] ; + sh:targetClass biolink:GeneToGeneCoexpressionAssociation . + +biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Set membership of a gene in a family of genes related by common evolutionary ancestry usually inferred by sequence comparisons. The genes in a given family generally share common sequence motifs which generally map onto shared gene product structure-function relationships." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 36 ; + sh:path dct:description ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "membership of the gene in the given gene family." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "membership of the gene in the given gene family." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:GeneFamily ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -16186,51 +16177,60 @@ biolink:GeneToGeneFamilyAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ] ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:GeneToGeneFamilyAssociation . biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; @@ -16238,123 +16238,68 @@ biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; sh:description "A homology association between two genes. May be orthology (in which case the species of subject and object should differ) or paralogy (in which case the species may be the same)" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "homology relationship type" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; @@ -16363,80 +16308,117 @@ biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "homology relationship type" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -16450,94 +16432,120 @@ biolink:GeneToGeneHomologyAssociation a sh:NodeShape ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ] ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ] ; sh:targetClass biolink:GeneToGeneHomologyAssociation . biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:closed true ; sh:description "A gene is transcribed and potentially translated to a gene product" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:GeneProductMixin ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:class biolink:Gene ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -16545,95 +16553,74 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:GeneProductMixin ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -16641,12 +16628,27 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -16654,35 +16656,33 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; sh:order 3 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; @@ -16694,63 +16694,88 @@ biolink:GeneToGeneProductRelationship a sh:NodeShape ; biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:class biolink:Gene ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -16758,87 +16783,68 @@ biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:Gene ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -16850,34 +16856,56 @@ biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -16885,181 +16913,172 @@ biolink:GeneToGoTermAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ] ; + sh:targetClass biolink:GeneToGoTermAssociation . + +biolink:GeneToPathwayAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An interaction between a gene or gene product and a biological process or pathway." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ] ; - sh:targetClass biolink:GeneToGoTermAssociation . - -biolink:GeneToPathwayAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An interaction between a gene or gene product and a biological process or pathway." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Pathway ; + sh:description "the pathway that includes or is affected by the gene or gene product" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the gene or gene product entity that participates or influences the pathway" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the gene or gene product entity that participates or influences the pathway" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -17067,213 +17086,155 @@ biolink:GeneToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Pathway ; - sh:description "the pathway that includes or is affected by the gene or gene product" ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ] ; + sh:order 32 ; + sh:path biolink:iri ] ; sh:targetClass biolink:GeneToPathwayAssociation . biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:subject_category ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:order 46 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 47 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 5 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:has_percentage ], + sh:order 50 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:GeneOrGeneProduct ; sh:description "gene in which variation is correlated with the phenotypic feature" ; sh:maxCount 1 ; @@ -17282,227 +17243,261 @@ biolink:GeneToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 35 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 46 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 49 ; + sh:path biolink:disease_context_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_count ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:deprecated ], + sh:order 33 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:has_quotient ], + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:has_total ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], + sh:order 31 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], + sh:order 47 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 40 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 48 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 45 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:id ], - [ sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:in ( "activity_or_abundance" "abundance" "activity" "expression" "synthesis" "degradation" "cleavage" "hydrolysis" "metabolic_processing" "mutation_rate" "stability" "folding" "localization" "transport" "absorption" "aggregation" "interaction" "release" "secretion" "uptake" "splicing" "molecular_interaction" "guanyl_nucleotide_exchange" "adenyl_nucleotide_exchange" "molecular_modification" "acetylation" "acylation" "alkylation" "amination" "carbamoylation" "ethylation" "glutathionylation" "glycation" "glycosylation" "glucuronidation" "n_linked_glycosylation" "o_linked_glycosylation" "hydroxylation" "lipidation" "farnesylation" "geranoylation" "myristoylation" "palmitoylation" "prenylation" "methylation" "nitrosation" "nucleotidylation" "phosphorylation" "ribosylation" "ADP-ribosylation" "sulfation" "sumoylation" "ubiquitination" "oxidation" "reduction" "carboxylation" ) ; + sh:order 41 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:subject_aspect_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:disease_context_qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:id ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 5 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 39 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ] ; + sh:order 7 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path rdf:type ] ; sh:targetClass biolink:GeneToPhenotypicFeatureAssociation . biolink:Genome a sh:NodeShape ; sh:closed true ; sh:description "A genome is the sum of genetic material within a cell or virion." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], + sh:order 9 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -17510,67 +17505,67 @@ biolink:Genome a sh:NodeShape ; sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 1 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ] ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Genome . biolink:GenomicBackgroundExposure a sh:NodeShape ; sh:closed true ; sh:description "A genomic background exposure is where an individual's specific genomic background of genes, sequence variants or other pre-existing genomic conditions constitute a kind of 'exposure' to the organism, leading to or influencing an outcome." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], + sh:order 17 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:full_name ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_gene_or_gene_product ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 8 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -17578,43 +17573,56 @@ biolink:GenomicBackgroundExposure a sh:NodeShape ; sh:order 4 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:order 0 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], + sh:order 18 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:synonym ], + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:xref ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 8 ; - sh:path biolink:has_quantitative_value ], + sh:order 6 ; + sh:path rdfs:label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:has_biological_sequence ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -17622,35 +17630,27 @@ biolink:GenomicBackgroundExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path biolink:provided_by ] ; + sh:path biolink:provided_by ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:GenomicBackgroundExposure . biolink:GenomicEntity a sh:NodeShape ; @@ -17668,85 +17668,119 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:closed true ; sh:description "A relationship between a sequence feature and a nucleic acid entity it is localized to. The reference entity may be a chromosome, chromosome region or information entity such as a contig." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:property [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; + sh:in ( "0" "1" "2" ) ; + sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:phase ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], + sh:order 35 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:object_namespace ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], + sh:order 37 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:integer ; - sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:end_interbase_coordinate ], + sh:order 33 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:order 31 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 41 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], + sh:order 11 ; + sh:path biolink:publications ], + [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; + sh:in ( "+" "-" "." "?" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:genome_build ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -17758,28 +17792,41 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:maxCount 1 ; sh:order 3 ; sh:path biolink:strand ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:object_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 35 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], + sh:order 36 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -17793,102 +17840,46 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 40 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:integer ; + sh:description "The position at which the subject nucleic acid entity ends on the chromosome or other entity to which it is located on." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], + sh:order 1 ; + sh:path biolink:end_interbase_coordinate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], + sh:order 24 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 9 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:id ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], + sh:order 13 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:integer ; sh:description "The position at which the subject nucleic acid entity starts on the chromosome or other entity to which it is located on. (ie: the start of the sequence being referenced is 0)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:start_interbase_coordinate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], - [ sh:description "The version of the genome on which a feature is located. For example, GRCh38 for Homo sapiens." ; - sh:in ( "+" "-" "." "?" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:genome_build ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:publications ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:negated ], [ sh:class biolink:NucleicAcidEntity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -17897,123 +17888,172 @@ biolink:GenomicSequenceLocalization a sh:NodeShape ; sh:order 5 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:description "The phase for a coding sequence entity. For example, phase of a CDS as represented in a GFF3 with a value of 0, 1 or 2." ; - sh:in ( "0" "1" "2" ) ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:order 4 ; - sh:path biolink:phase ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path dct:description ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ] ; + sh:order 19 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ] ; sh:targetClass biolink:GenomicSequenceLocalization . biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 44 ; + sh:path biolink:disease_context_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 43 ; + sh:path biolink:qualified_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:Genotype ; + sh:description "A genotype that has a role in modeling the disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -18021,250 +18061,158 @@ biolink:GenotypeAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 23 ; sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:Genotype ; - sh:description "A genotype that has a role in modeling the disease." ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Disease ; - sh:description "disease" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 44 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ] ; - sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . - -biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 44 ; - sh:path biolink:disease_context_qualifier ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:frequency_qualifier ], + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 36 ; + sh:path dct:description ] ; + sh:targetClass biolink:GenotypeAsAModelOfDiseaseAssociation . + +biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:class biolink:Disease ; sh:description "a disease that is associated with that genotype" ; sh:maxCount 1 ; @@ -18278,11 +18226,12 @@ biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:order 19 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:Genotype ; sh:description "a genotype that is associated in some way with a disease state" ; sh:maxCount 1 ; @@ -18290,137 +18239,199 @@ biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 44 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "E.g. is pathogenic for" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 45 ; + sh:path biolink:frequency_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 43 ; + sh:path biolink:qualified_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; @@ -18432,34 +18443,30 @@ biolink:GenotypeToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ] ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:GenotypeToDiseaseAssociation . biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Genotype ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:Genotype ; sh:description "genotype that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -18472,99 +18479,102 @@ biolink:GenotypeToEntityAssociationMixin a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:object ] ; sh:targetClass biolink:GenotypeToEntityAssociationMixin . biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between a genotype and a gene. The genotype have have multiple variants in that gene or a single one. There is no assumption of cardinality" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:property [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "the relationship type used to connect genotype to gene" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -18572,29 +18582,11 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Gene ; sh:description "gene implicated in genotype" ; sh:maxCount 1 ; @@ -18603,74 +18595,73 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:order 2 ; sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -18678,49 +18669,82 @@ biolink:GenotypeToGeneAssociation a sh:NodeShape ; sh:order 36 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ] ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:GenotypeToGeneAssociation . biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between one genotype and a genotypic entity that is a sub-component of it" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -18728,83 +18752,101 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:order 15 ; sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:Genotype ; sh:description "child genotype" ; sh:maxCount 1 ; @@ -18812,291 +18854,290 @@ biolink:GenotypeToGenotypePartAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Genotype ; - sh:description "parent genotype" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Genotype ; + sh:description "parent genotype" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ] ; + sh:order 14 ; + sh:path biolink:original_subject ] ; sh:targetClass biolink:GenotypeToGenotypePartAssociation . biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between one genotype and a phenotypic feature, where having the genotype confers the phenotype, either in isolation or through environment" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Genotype ; - sh:description "genotype that is associated with the phenotypic feature" ; + sh:property [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 41 ; + sh:path biolink:has_total ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:double ; sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:has_percentage ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 49 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:double ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 50 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 46 ; sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 3 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_count ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 37 ; sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -19108,77 +19149,64 @@ biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 35 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:double ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:has_quotient ], + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:class biolink:Genotype ; + sh:description "genotype that is associated with the phenotypic feature" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 32 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -19186,157 +19214,132 @@ biolink:GenotypeToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 4 ; sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:disease_context_qualifier ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:order 48 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ] ; + sh:path biolink:subject_closure ] ; sh:targetClass biolink:GenotypeToPhenotypicFeatureAssociation . biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:closed true ; sh:description "Any association between a genotype and a sequence variant." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:property [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:SequenceVariant ; + sh:description "gene implicated in genotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:class biolink:SequenceVariant ; - sh:description "gene implicated in genotype" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Genotype ; sh:description "parent genotype" ; sh:maxCount 1 ; @@ -19345,35 +19348,53 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "the relationship type used to connect genotype to gene" ; sh:maxCount 1 ; @@ -19381,66 +19402,45 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -19449,33 +19449,34 @@ biolink:GenotypeToVariantAssociation a sh:NodeShape ; sh:order 31 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ] ; + sh:order 11 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:GenotypeToVariantAssociation . biolink:GenotypicSex a sh:NodeShape ; sh:closed true ; sh:description "An attribute corresponding to the genotypic sex of the individual, based upon genotypic composition of sex chromosomes." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -19483,11 +19484,10 @@ biolink:GenotypicSex a sh:NodeShape ; sh:order 10 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; @@ -19513,16 +19513,38 @@ biolink:GenotypicSex a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -19530,63 +19552,50 @@ biolink:GenotypicSex a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ] ; + sh:path rdf:type ] ; sh:targetClass biolink:GenotypicSex . biolink:GeographicExposure a sh:NodeShape ; sh:closed true ; sh:description "A geographic exposure is a factor relating to geographic proximity to some impactful entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -19594,29 +19603,29 @@ biolink:GeographicExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -19627,32 +19636,23 @@ biolink:GeographicExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ] ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ] ; sh:targetClass biolink:GeographicExposure . biolink:GeographicLocation a sh:NodeShape ; @@ -19660,40 +19660,56 @@ biolink:GeographicLocation a sh:NodeShape ; sh:description "a location that can be described in lat/long coordinates" ; sh:ignoredProperties ( rdf:type biolink:timepoint ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -19705,51 +19721,52 @@ biolink:GeographicLocation a sh:NodeShape ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:float ; - sh:description "longitude" ; + sh:description "latitude" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:longitude ], + sh:order 0 ; + sh:path biolink:latitude ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:float ; - sh:description "latitude" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:latitude ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "longitude" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:order 1 ; + sh:path biolink:longitude ] ; sh:targetClass biolink:GeographicLocation . biolink:GeographicLocationAtTime a sh:NodeShape ; sh:closed true ; sh:description "a location that can be described in lat/long coordinates, for a particular time" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:float ; sh:description "longitude" ; sh:maxCount 1 ; @@ -19764,48 +19781,42 @@ biolink:GeographicLocationAtTime a sh:NodeShape ; sh:order 7 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:float ; + sh:description "latitude" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path biolink:latitude ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -19813,38 +19824,48 @@ biolink:GeographicLocationAtTime a sh:NodeShape ; sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:float ; - sh:description "latitude" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:latitude ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ] ; + sh:order 8 ; + sh:path biolink:iri ] ; sh:targetClass biolink:GeographicLocationAtTime . biolink:GrossAnatomicalStructure a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -19856,19 +19877,6 @@ biolink:GrossAnatomicalStructure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -19881,31 +19889,23 @@ biolink:GrossAnatomicalStructure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -19919,66 +19919,39 @@ biolink:Haplotype a sh:NodeShape ; sh:description "A set of zero or more Alleles on a single instance of a Sequence[VMC]" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -19986,37 +19959,65 @@ biolink:Haplotype a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:Haplotype . biolink:Hospitalization a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], + sh:property [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 7 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -20024,10 +20025,11 @@ biolink:Hospitalization a sh:NodeShape ; sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -20041,39 +20043,37 @@ biolink:Hospitalization a sh:NodeShape ; sh:order 6 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:order 8 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Hospitalization . biolink:HospitalizationOutcome a sh:NodeShape ; @@ -20087,11 +20087,21 @@ biolink:Human a sh:NodeShape ; sh:description "A member of the the species Homo sapiens." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; @@ -20103,191 +20113,221 @@ biolink:Human a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ] ; + sh:order 7 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Human . biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:closed true ; sh:description "association between a named thing and a information content entity where the specific context of the relationship between that named thing and the publication is unknown. For example, model organisms databases often capture the knowledge that a gene is found in a journal article, but not specifically the context in which that gene was documented in the article. In these cases, this association with the accompanying predicate 'mentions' could be used. Conversely, for more specific associations (like 'gene to disease association', the publication should be captured as an edge property)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:property [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -20295,85 +20335,46 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 33 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -20381,34 +20382,24 @@ biolink:InformationContentEntityToNamedThingAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ] ; + sh:order 38 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:InformationContentEntityToNamedThingAssociation . biolink:Invertebrate a sh:NodeShape ; sh:closed true ; sh:description "An animal lacking a vertebral column. This group consists of 98% of all animal species." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; + sh:property [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; @@ -20425,12 +20416,22 @@ biolink:Invertebrate a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -20438,74 +20439,78 @@ biolink:Invertebrate a sh:NodeShape ; sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:Invertebrate . biolink:JournalArticle a sh:NodeShape ; sh:closed true ; sh:description "an article, typically presenting results of research, that is published in an issue of a scientific journal." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:license ], + sh:order 9 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:iso_abbreviation ], + sh:order 0 ; + sh:path biolink:published_in ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:pages ], + sh:order 22 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; @@ -20513,121 +20518,116 @@ biolink:JournalArticle a sh:NodeShape ; sh:order 6 ; sh:path biolink:summary ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Optional value, if used locally as a convenience, is set to the iso abbreviation of the 'published in' parent." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:full_name ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:authors ], - [ sh:datatype xsd:anyURI ; - sh:description "The enclosing parent serial containing the article should have industry-standard identifier from ISSN." ; + sh:order 1 ; + sh:path biolink:iso_abbreviation ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:issue ], + [ sh:datatype xsd:string ; + sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:volume ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:published_in ], + sh:order 20 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:rights ], [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:creation_date ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:xref ], + sh:order 19 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:keywords ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path dct:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:synonym ], + sh:order 23 ; + sh:path dct:description ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:issue ], + sh:order 16 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:iri ], + sh:order 15 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:license ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:format ], + sh:order 18 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; - sh:maxCount 1 ; + sh:order 17 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:volume ] ; + sh:order 8 ; + sh:path biolink:mesh_terms ] ; sh:targetClass biolink:JournalArticle . biolink:LogOddsAnalysisResult a sh:NodeShape ; @@ -20635,15 +20635,37 @@ biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:description "A result of a log odds ratio analysis." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 13 ; + sh:path dct:description ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -20655,12 +20677,22 @@ biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -20672,89 +20704,41 @@ biolink:LogOddsAnalysisResult a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ] ; + sh:path biolink:id ] ; sh:targetClass biolink:LogOddsAnalysisResult . biolink:MacromolecularComplex a sh:NodeShape ; sh:closed true ; sh:description "A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -20762,23 +20746,19 @@ biolink:MacromolecularComplex a sh:NodeShape ; sh:order 8 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -20786,63 +20766,109 @@ biolink:MacromolecularComplex a sh:NodeShape ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ] ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:MacromolecularComplex . biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a biological process or pathway (as represented in the GO biological process branch), where the entity carries out some part of the process, regulates it, or acts upstream of it." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:class biolink:BiologicalProcess ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -20850,214 +20876,183 @@ biolink:MacromolecularMachineToBiologicalProcessAssociation a sh:NodeShape ; sh:order 30 ; sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:species_context_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:BiologicalProcess ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 28 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:deprecated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 13 ; sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:species_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 35 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ] ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ] ; sh:targetClass biolink:MacromolecularMachineToBiologicalProcessAssociation . biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a cellular component (as represented in the GO cellular component branch), where the entity carries out its function in the cellular component." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; @@ -21065,132 +21060,141 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:order 5 ; sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:species_context_qualifier ], - [ sh:class biolink:CellularComponent ; - sh:description "class describing the activity, process or localization of the gene product" ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 34 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:species_context_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -21198,235 +21202,198 @@ biolink:MacromolecularMachineToCellularComponentAssociation a sh:NodeShape ; sh:order 13 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], + sh:order 17 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:CellularComponent ; + sh:description "class describing the activity, process or localization of the gene product" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:order 29 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ] ; + sh:order 4 ; + sh:path biolink:negated ] ; sh:targetClass biolink:MacromolecularMachineToCellularComponentAssociation . biolink:MacromolecularMachineToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:description "an association which has a macromolecular machine mixin as a subject" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:species_context_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:NamedThing ; + sh:property [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:species_context_qualifier ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:MacromolecularMachineToEntityAssociationMixin . biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:closed true ; sh:description "A functional association between a macromolecular machine (gene, gene product or complex) and a molecular activity (as represented in the GO molecular function branch), where the entity carries out the activity, or contributes to its execution." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; + sh:property [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:species_context_qualifier ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:class biolink:MolecularActivity ; - sh:description "class describing the activity, process or localization of the gene product" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 8 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -21434,116 +21401,149 @@ biolink:MacromolecularMachineToMolecularActivityAssociation a sh:NodeShape ; sh:order 39 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 3 ; + sh:path biolink:species_context_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 33 ; + sh:path biolink:iri ], + [ sh:class biolink:MolecularActivity ; + sh:description "class describing the activity, process or localization of the gene product" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:MacromolecularMachineMixin ; - sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], + sh:order 7 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:MacromolecularMachineMixin ; + sh:description "gene, product or macromolecular complex that has the function associated with the GO term" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ] ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ] ; sh:targetClass biolink:MacromolecularMachineToMolecularActivityAssociation . biolink:Mammal a sh:NodeShape ; @@ -21551,11 +21551,34 @@ biolink:Mammal a sh:NodeShape ; sh:description "A member of the class Mammalia, a clade of endothermic amniotes distinguished from reptiles and birds by the possession of hair, three middle ear bones, mammary glands, and a neocortex" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -21563,6 +21586,17 @@ biolink:Mammal a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -21570,64 +21604,30 @@ biolink:Mammal a sh:NodeShape ; sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ] ; + sh:order 9 ; + sh:path rdf:type ] ; sh:targetClass biolink:Mammal . biolink:MappingCollection a sh:NodeShape ; @@ -21646,83 +21646,64 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:description "An association between a material sample and the material entity from which it is derived." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "derivation relationship" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:NamedThing ; sh:description "the material entity the sample was derived from. This may be another material sample, or any other material entity, including for example an organism, a geographic feature, or some environmental material." ; sh:maxCount 1 ; @@ -21730,49 +21711,42 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "derivation relationship" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:MaterialSample ; sh:description "the material sample being described" ; sh:maxCount 1 ; @@ -21780,94 +21754,120 @@ biolink:MaterialSampleDerivationAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ] ; + sh:order 33 ; + sh:path biolink:category ] ; sh:targetClass biolink:MaterialSampleDerivationAssociation . biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; @@ -21880,89 +21880,46 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:anyURI ; - sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_specialization_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 41 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 15 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], + sh:order 4 ; + sh:path biolink:subject_specialization_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], + sh:order 12 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:Disease ; sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; @@ -21973,26 +21930,24 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "A qualifier that composes with a core subject/object concept to define a more specific version of the subject concept, specifically using an ontology term that is not a subclass or descendant of the core concept and in the vast majority of cases, is of a different ontological namespace than the category or namespace of the subject identifier." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:subject_specialization_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:qualifiers ], + sh:order 5 ; + sh:path biolink:object_specialization_qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 20 ; + sh:path biolink:original_object ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -22000,58 +21955,56 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "disease or phenotype" ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:anatomical_context_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:subject_label_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 40 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -22059,18 +22012,21 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 13 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:order 27 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], + sh:order 37 ; + sh:path biolink:category ], [ sh:class biolink:MaterialSample ; sh:description "the material sample being described" ; sh:maxCount 1 ; @@ -22078,49 +22034,93 @@ biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:object_label_closure ], + sh:order 36 ; + sh:path biolink:iri ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "disease or phenotype" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ] ; + sh:order 26 ; + sh:path biolink:object_category_closure ] ; sh:targetClass biolink:MaterialSampleToDiseaseOrPhenotypicFeatureAssociation . biolink:MaterialSampleToEntityAssociationMixin a sh:NodeShape ; @@ -22154,38 +22154,38 @@ biolink:MicroRNA a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -22193,44 +22193,44 @@ biolink:MicroRNA a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ] ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ] ; sh:targetClass biolink:MicroRNA . biolink:ModelToDiseaseAssociationMixin a sh:NodeShape ; @@ -22265,39 +22265,80 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:ChemicalEntity ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -22305,6 +22346,24 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:MolecularActivity ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -22312,591 +22371,563 @@ biolink:MolecularActivityToChemicalEntityAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:path biolink:qualifiers ] ; + sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . + +biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; - sh:targetClass biolink:MolecularActivityToChemicalEntityAssociation . - -biolink:MolecularActivityToMolecularActivityAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Added in response to capturing relationship between microbiome activities as measured via measurements of blood analytes as collected via blood and stool samples" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:RetrievalSource ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:path biolink:id ] ; + sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . + +biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:Pathway ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ] ; - sh:targetClass biolink:MolecularActivityToMolecularActivityAssociation . - -biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "Association that holds the relationship between a reaction and the pathway it participates in." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:MolecularActivity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:MolecularActivity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -22908,89 +22939,26 @@ biolink:MolecularActivityToPathwayAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Pathway ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ] ; + sh:order 11 ; + sh:path biolink:knowledge_level ] ; sh:targetClass biolink:MolecularActivityToPathwayAssociation . biolink:MolecularMixture a sh:NodeShape ; sh:closed true ; sh:description "A molecular mixture is a chemical mixture composed of two or more molecular entities with known concentration and stoichiometry." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; - sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; - sh:order 3 ; - sh:path biolink:routes_of_delivery ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], + sh:property [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -23000,46 +22968,36 @@ biolink:MolecularMixture a sh:NodeShape ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 4 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:category ], + sh:order 17 ; + sh:path rdfs:label ], [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; sh:maxCount 1 ; sh:order 1 ; sh:path biolink:highest_FDA_approval_status ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:full_name ], + sh:order 14 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_chemical_role ], + sh:order 11 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -23047,24 +23005,66 @@ biolink:MolecularMixture a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; + sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; + sh:order 3 ; + sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_supplement ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:is_toxic ] ; + sh:path biolink:is_toxic ], + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_chemical_role ] ; sh:targetClass biolink:MolecularMixture . biolink:MortalityOutcome a sh:NodeShape ; @@ -23077,198 +23077,166 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path rdf:predicate ], - [ sh:class biolink:Publication ; + sh:property [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path rdf:type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 32 ; - sh:path biolink:retrieval_source_ids ], + sh:order 4 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 13 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], + sh:order 19 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 37 ; + sh:path biolink:iri ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 35 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:object_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], + sh:order 9 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:object_category ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], + sh:order 2 ; + sh:path biolink:subject_context_qualifier ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:population_context_qualifier ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:deprecated ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 8 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:object_context_qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 42 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 32 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:p_value ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "a biological population (general, study, cohort, etc.) with a specific set of characteristics to constrain an association." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:population_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_subject ], + sh:order 40 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -23276,24 +23244,60 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:subject_context_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 10 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], + sh:order 3 ; + sh:path rdf:predicate ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -23301,39 +23305,57 @@ biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation a sh:NodeShape sh:order 17 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:subject_label_closure ], + sh:order 18 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ] ; + sh:order 29 ; + sh:path biolink:object_namespace ] ; sh:targetClass biolink:NamedThingAssociatedWithLikelihoodOfNamedThingAssociation . biolink:NoncodingRNAProduct a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; @@ -23353,136 +23375,115 @@ biolink:NoncodingRNAProduct a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ] ; + sh:order 1 ; + sh:path biolink:xref ] ; sh:targetClass biolink:NoncodingRNAProduct . biolink:NucleicAcidSequenceMotif a sh:NodeShape ; sh:closed true ; sh:description "A linear nucleotide sequence pattern that is widespread and has, or is conjectured to have, a biological significance. e.g. the TATA box promoter motif, transcription factor binding consensus sequences." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -23490,39 +23491,28 @@ biolink:NucleicAcidSequenceMotif a sh:NodeShape ; sh:order 10 ; sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ] ; + sh:order 3 ; + sh:path biolink:xref ] ; sh:targetClass biolink:NucleicAcidSequenceMotif . biolink:NucleosomeModification a sh:NodeShape ; sh:closed true ; sh:description "A chemical modification of a histone protein within a nucleosome octomer or a substitution of a histone with a variant histone isoform. e.g. Histone 4 Lysine 20 methylation (H4K20me), histone variant H2AZ substituting H2A." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -23530,20 +23520,32 @@ biolink:NucleosomeModification a sh:NodeShape ; sh:order 5 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -23551,68 +23553,55 @@ biolink:NucleosomeModification a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ] ; + sh:order 3 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:NucleosomeModification . biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a observed expected frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -23621,64 +23610,75 @@ biolink:ObservedExpectedFrequencyAnalysisResult a sh:NodeShape ; sh:order 8 ; sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 0 ; + sh:path biolink:license ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; - sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ] ; + sh:order 11 ; + sh:path rdf:type ] ; sh:targetClass biolink:ObservedExpectedFrequencyAnalysisResult . biolink:Occurrent a sh:NodeShape ; @@ -23691,149 +23691,217 @@ biolink:OrganismAttribute a sh:NodeShape ; sh:closed true ; sh:description "describes a characteristic of an organismal entity." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; + sh:property [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ] ; + sh:order 5 ; + sh:path biolink:id ] ; sh:targetClass biolink:OrganismAttribute . biolink:OrganismTaxonToEntityAssociation a sh:NodeShape ; sh:closed false ; sh:description "An association between an organism taxon and another entity" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; + sh:property [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OrganismTaxon ; sh:description "organism taxon that is the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 0 ; + sh:path rdf:subject ] ; + sh:targetClass biolink:OrganismTaxonToEntityAssociation . + +biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; + sh:closed false ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ] ; - sh:targetClass biolink:OrganismTaxonToEntityAssociation . - -biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; - sh:closed false ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -23841,82 +23909,82 @@ biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:NamedThing ; + sh:description "the environment in which the organism occurs" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 2 ; + sh:path rdf:object ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "predicate describing the relationship between the taxon and the environment" ; sh:maxCount 1 ; @@ -23925,477 +23993,375 @@ biolink:OrganismTaxonToEnvironmentAssociation a sh:NodeShape ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:NamedThing ; - sh:description "the environment in which the organism occurs" ; + sh:order 32 ; + sh:path biolink:iri ] ; + sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . + +biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; + sh:closed false ; + sh:description "A relationship between two organism taxon nodes" ; + sh:ignoredProperties ( rdf:type biolink:associated_environmental_context ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OrganismTaxon ; + sh:description "organism taxon that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ] ; - sh:targetClass biolink:OrganismTaxonToEnvironmentAssociation . - -biolink:OrganismTaxonToOrganismTaxonAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "A relationship between two organism taxon nodes" ; - sh:ignoredProperties ( rdf:type biolink:associated_environmental_context ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "organism taxon that is the subject of the association" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 28 ; sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ] ; + sh:order 20 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:OrganismTaxonToOrganismTaxonAssociation . biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction relationship between two taxa. This may be a symbiotic relationship (encompassing mutualism and parasitism), or it may be non-symbiotic. Example: plague transmitted_by flea; cattle domesticated_by Homo sapiens; plague infects Homo sapiens" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], + sh:property [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdf:type ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 21 ; sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "the environment in which the two taxa interact" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:associated_environmental_context ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 20 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:p_value ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the taxon that is the subject of the association" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], + sh:order 2 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "the environment in which the two taxa interact" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 0 ; + sh:path biolink:associated_environmental_context ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OrganismTaxon ; sh:description "the taxon that is the subject of the association" ; sh:maxCount 1 ; @@ -24403,293 +24369,296 @@ biolink:OrganismTaxonToOrganismTaxonInteraction a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:order 32 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 34 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 17 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the taxon that is the subject of the association" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:negated ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . - -biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; - sh:closed true ; - sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 30 ; + sh:order 31 ; sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 5 ; + sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more general taxon" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; + sh:order 12 ; sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 9 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonInteraction . + +biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; + sh:closed true ; + sh:description "A child-parent relationship between two taxa. For example: Homo sapiens subclass_of Homo" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the more specific taxon" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:class biolink:OrganismTaxon ; - sh:description "the more specific taxon" ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; @@ -24700,136 +24669,139 @@ biolink:OrganismTaxonToOrganismTaxonSpecialization a sh:NodeShape ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . - -biolink:OrganismToOrganismAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OrganismTaxon ; + sh:description "the more general taxon" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 2 ; + sh:path rdf:object ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:path biolink:retrieval_source_ids ] ; + sh:targetClass biolink:OrganismTaxonToOrganismTaxonSpecialization . + +biolink:OrganismToOrganismAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:class biolink:IndividualOrganism ; + sh:description "An association between two individual organisms." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; @@ -24837,115 +24809,143 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; sh:order 28 ; sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:IndividualOrganism ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:IndividualOrganism ; - sh:description "An association between two individual organisms." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:IndividualOrganism ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -24957,129 +24957,159 @@ biolink:OrganismToOrganismAssociation a sh:NodeShape ; biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 45 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 44 ; - sh:path biolink:disease_context_qualifier ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 44 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 26 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:class biolink:Disease ; sh:description "disease" ; sh:maxCount 1 ; @@ -25087,287 +25117,262 @@ biolink:OrganismalEntityAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OrganismalEntity ; - sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:frequency_qualifier ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OrganismalEntity ; + sh:description "A organismal entity (strain, breed) with a predisposition to a disease, or bred/created specifically to model a disease." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 43 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ] ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:OrganismalEntityAsAModelOfDiseaseAssociation . biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction between two genes or two gene products. May be physical (e.g. protein binding) or genetic (between genes). May be symmetric (e.g. protein interaction) or directed (e.g. phosphorylation)" ; sh:ignoredProperties ( rdf:type biolink:interacting_molecules_category ) ; - sh:property [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; + sh:property [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "interaction relationship type" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "interaction relationship type" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -25375,241 +25380,194 @@ biolink:PairwiseGeneToGeneInteraction a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ] ; + sh:order 15 ; + sh:path biolink:original_predicate ] ; sh:targetClass biolink:PairwiseGeneToGeneInteraction . biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:closed true ; sh:description "An interaction at the molecular level between two physical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:MolecularEntity ; - sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:property [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "interaction relationship type" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:interacting_molecules_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:subject_namespace ], - [ sh:class biolink:MolecularEntity ; - sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 37 ; + sh:path dct:description ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], + sh:order 17 ; + sh:path biolink:original_object ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 38 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "identifier for the interaction. This may come from an interaction database such as IMEX." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:order 32 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "interaction relationship type" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:order 2 ; + sh:path rdf:predicate ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -25617,72 +25575,114 @@ biolink:PairwiseMolecularInteraction a sh:NodeShape ; sh:order 10 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:MolecularEntity ; + sh:description "the object gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:order 5 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 21 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 36 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdf:type ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:class biolink:OntologyClass ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:order 0 ; + sh:path biolink:interacting_molecules_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ] ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:class biolink:MolecularEntity ; + sh:description "the subject gene in the association. If the relation is symmetric, subject vs object is arbitrary. We allow a gene product to stand as a proxy for the gene or vice versa." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ] ; sh:targetClass biolink:PairwiseMolecularInteraction . biolink:Patent a sh:NodeShape ; @@ -25690,65 +25690,67 @@ biolink:Patent a sh:NodeShape ; sh:description "a legal document granted by a patent issuing authority which confers upon the patenter the sole right to make, use and sell an invention for a set period of time." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 14 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path dct:type ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 3 ; + sh:path biolink:keywords ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], + sh:order 21 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], + sh:order 2 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; @@ -25756,59 +25758,57 @@ biolink:Patent a sh:NodeShape ; sh:order 18 ; sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:order 13 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], + sh:order 19 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + sh:order 11 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], + sh:order 17 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; - sh:path biolink:category ] ; + sh:path biolink:category ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Patent . biolink:PathognomonicityQuantifier a sh:NodeShape ; @@ -25822,51 +25822,45 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:description "An abnormal anatomical structure, when viewed as an exposure, representing an precondition, leading to or influencing an outcome, e.g. thrombosis leading to an ischemic disease outcome." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -25874,17 +25868,28 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -25896,22 +25901,17 @@ biolink:PathologicalAnatomicalExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ] ; + sh:order 7 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:PathologicalAnatomicalExposure . biolink:PathologicalAnatomicalOutcome a sh:NodeShape ; @@ -25924,24 +25924,12 @@ biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:closed true ; sh:description "An anatomical structure with the potential of have an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -25949,59 +25937,71 @@ biolink:PathologicalAnatomicalStructure a sh:NodeShape ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ] ; + sh:path dct:description ] ; sh:targetClass biolink:PathologicalAnatomicalStructure . biolink:PathologicalEntityMixin a sh:NodeShape ; @@ -26015,60 +26015,37 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:description "A biologic function or a process having an abnormal or deleterious effect at the subcellular, cellular, multicellular, or organismal level." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -26076,49 +26053,71 @@ biolink:PathologicalProcess a sh:NodeShape ; sh:order 14 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 10 ; + sh:path biolink:iri ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:PathologicalProcess . biolink:PathologicalProcessExposure a sh:NodeShape ; sh:closed true ; sh:description "A pathological process, when viewed as an exposure, representing a precondition, leading to or influencing an outcome, e.g. autoimmunity leading to disease." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:property [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 3 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -26126,43 +26125,43 @@ biolink:PathologicalProcessExposure a sh:NodeShape ; sh:order 13 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdfs:label ], + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -26170,21 +26169,29 @@ biolink:PathologicalProcessExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 3 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -26192,18 +26199,11 @@ biolink:PathologicalProcessExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ] ; + sh:order 8 ; + sh:path biolink:xref ] ; sh:targetClass biolink:PathologicalProcessExposure . biolink:PathologicalProcessOutcome a sh:NodeShape ; @@ -26223,49 +26223,43 @@ biolink:Phenomenon a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -26273,84 +26267,55 @@ biolink:Phenomenon a sh:NodeShape ; sh:order 11 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 5 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ] ; + sh:order 8 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Phenomenon . biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 49 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 43 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -26359,60 +26324,76 @@ biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:order 32 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 13 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:object_label_closure ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 50 ; - sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:class biolink:Disease ; + sh:description "disease" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path biolink:original_object ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], [ sh:class biolink:PhenotypicFeature ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -26420,166 +26401,185 @@ biolink:PhenotypicFeatureToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 0 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdf:type ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 37 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:object_category_closure ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 47 ; sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 48 ; sh:path biolink:qualified_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:object_category ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 45 ; sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:integer ; sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:has_total ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 49 ; - sh:path biolink:frequency_qualifier ], + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_quotient ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 50 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:nodeKind sh:Literal ; + sh:order 39 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ] ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:PhenotypicFeatureToDiseaseAssociation . biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; @@ -26590,19 +26590,6 @@ biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:maxCount 1 ; sh:order 6 ; sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path rdf:subject ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; @@ -26614,12 +26601,25 @@ biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:has_total ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 11 ; + sh:path rdf:subject ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 10 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:integer ; sh:description "number of things with a particular property" ; sh:maxCount 1 ; @@ -26627,48 +26627,48 @@ biolink:PhenotypicFeatureToEntityAssociationMixin a sh:NodeShape ; sh:order 1 ; sh:path biolink:has_count ], [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], + sh:order 3 ; + sh:path biolink:has_quotient ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:qualified_predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path rdf:object ], - [ sh:datatype xsd:double ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_quotient ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:frequency_qualifier ], + sh:order 7 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path rdf:predicate ] ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:subject_aspect_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path rdf:object ] ; sh:targetClass biolink:PhenotypicFeatureToEntityAssociationMixin . biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; @@ -26676,171 +26676,173 @@ biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; sh:description "Association between two concept nodes of phenotypic character, qualified by the predicate used. This association may typically be used to specify 'similar_to' or 'member_of' relationships." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_count ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 29 ; + sh:path biolink:p_value ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 36 ; + sh:path rdfs:label ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 13 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:sex_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], + sh:order 2 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], + sh:order 48 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 41 ; + sh:path biolink:has_total ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:order 3 ; + sh:path rdf:object ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], + sh:order 39 ; + sh:path biolink:deprecated ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:sex_qualifier ], + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], + sh:order 37 ; + sh:path dct:description ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 40 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 43 ; + sh:path biolink:has_percentage ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:negated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category_closure ], + sh:order 23 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:publications ], + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], + sh:order 20 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:qualifiers ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:knowledge_level ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -26848,216 +26850,214 @@ biolink:PhenotypicFeatureToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:id ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; - sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_total ], + sh:order 33 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 26 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 28 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:publications ], + sh:order 49 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_label_closure ], [ sh:datatype ; sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 50 ; sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path dct:description ], + sh:order 16 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 15 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_quotient ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; - sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:object ], + sh:order 8 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path biolink:original_object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 31 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path rdf:subject ], + sh:order 13 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:category ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:object_category_closure ], + sh:order 22 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ] ; + sh:order 21 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:PhenotypicFeatureToPhenotypicFeatureAssociation . biolink:PhenotypicQuality a sh:NodeShape ; sh:closed true ; sh:description "A property of a phenotype" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:provided_by ] ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ] ; sh:targetClass biolink:PhenotypicQuality . biolink:PhenotypicSex a sh:NodeShape ; @@ -27065,33 +27065,48 @@ biolink:PhenotypicSex a sh:NodeShape ; sh:description "An attribute corresponding to the phenotypic sex of the individual, based upon the reproductive organs present." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:NamedThing ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -27099,21 +27114,11 @@ biolink:PhenotypicSex a sh:NodeShape ; sh:order 4 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -27121,34 +27126,29 @@ biolink:PhenotypicSex a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ] ; + sh:order 10 ; + sh:path biolink:category ] ; sh:targetClass biolink:PhenotypicSex . biolink:PhysicalEssence a sh:NodeShape ; @@ -27167,17 +27167,26 @@ biolink:PhysiologicalProcess a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], + sh:order 5 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -27189,88 +27198,89 @@ biolink:PhysiologicalProcess a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 0 ; + sh:path biolink:id ], [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:order 13 ; + sh:path rdfs:label ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], + sh:order 2 ; + sh:path biolink:has_output ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ] ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:PhysiologicalProcess . biolink:PlanetaryEntity a sh:NodeShape ; sh:closed true ; sh:description "Any entity or process that exists at the level of the whole planet" ; - sh:ignoredProperties ( rdf:type biolink:latitude biolink:timepoint biolink:longitude ) ; + sh:ignoredProperties ( biolink:longitude rdf:type biolink:latitude biolink:timepoint ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -27278,113 +27288,104 @@ biolink:PlanetaryEntity a sh:NodeShape ; sh:order 6 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ] ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:PlanetaryEntity . biolink:Plant a sh:NodeShape ; sh:closed true ; sh:description "" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -27392,6 +27393,17 @@ biolink:Plant a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -27403,46 +27415,45 @@ biolink:Plant a sh:NodeShape ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ] ; + sh:path biolink:category ] ; sh:targetClass biolink:Plant . biolink:Polypeptide a sh:NodeShape ; sh:closed true ; sh:description "A polypeptide is a molecular entity characterized by availability in protein databases of amino-acid-based sequence representations of its precise primary structure; for convenience of representation, partial sequences of various kinds are included, even if they do not represent a physical molecule." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:Attribute ; + sh:property [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -27450,51 +27461,40 @@ biolink:Polypeptide a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -27506,122 +27506,73 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a two populations" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 36 ; + sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the subject of the association" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that form the object of the association" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A relationship type that holds between the subject and object populations. Standard mereological relations can be used. E.g. subject part-of object, subject overlaps object. Derivation relationships can also be used" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the subject of the association" ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; @@ -27629,10 +27580,17 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; @@ -27644,113 +27602,144 @@ biolink:PopulationToPopulationAssociation a sh:NodeShape ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that form the object of the association" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 25 ; + sh:path biolink:subject_label_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 3 ; + sh:path biolink:negated ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:subject_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ] ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ] ; sh:targetClass biolink:PopulationToPopulationAssociation . biolink:PosttranslationalModification a sh:NodeShape ; sh:closed true ; sh:description "A chemical modification of a polypeptide or protein that occurs after translation. e.g. polypeptide cleavage to form separate proteins, methylation or acetylation of histone tail amino acids, protein ubiquitination." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -27758,154 +27747,140 @@ biolink:PosttranslationalModification a sh:NodeShape ; sh:order 1 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:PosttranslationalModification . - -biolink:PreprintPublication a sh:NodeShape ; - sh:closed true ; - sh:description "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "keywords tagging a publication" ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:keywords ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ] ; + sh:targetClass biolink:PosttranslationalModification . + +biolink:PreprintPublication a sh:NodeShape ; + sh:closed true ; + sh:description "a document reresenting an early version of an author's original scholarly work, such as a research paper or a review, prior to formal peer review and publication in a peer-reviewed scholarly or scientific journal." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:order 8 ; + sh:path biolink:rights ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ], + sh:order 10 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; + sh:order 6 ; + sh:path dct:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:order 1 ; + sh:path biolink:pages ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], + sh:order 2 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 16 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -27913,32 +27888,57 @@ biolink:PreprintPublication a sh:NodeShape ; sh:order 19 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], + sh:order 9 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "keywords tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:keywords ], [ sh:datatype xsd:anyURI ; sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], + sh:order 18 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; - sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ] ; + sh:order 17 ; + sh:path rdf:type ] ; sh:targetClass biolink:PreprintPublication . biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; @@ -27951,38 +27951,16 @@ biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; @@ -27990,68 +27968,59 @@ biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:order 11 ; sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -28059,34 +28028,46 @@ biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:BiologicalProcess ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:class biolink:BiologicalProcess ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -28094,80 +28075,99 @@ biolink:ProcessRegulatesProcessAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:BiologicalProcess ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ] ; + sh:order 3 ; + sh:path biolink:negated ] ; sh:targetClass biolink:ProcessRegulatesProcessAssociation . biolink:ProcessedMaterial a sh:NodeShape ; @@ -28175,44 +28175,17 @@ biolink:ProcessedMaterial a sh:NodeShape ; sh:description "A chemical entity (often a mixture) processed for consumption for nutritional, medical or technical use. Is a material entity that is created or changed during material processing." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:trade_name ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 5 ; - sh:path biolink:available_from ], + sh:order 7 ; + sh:path biolink:is_toxic ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; @@ -28224,32 +28197,11 @@ biolink:ProcessedMaterial a sh:NodeShape ; sh:order 1 ; sh:path biolink:highest_FDA_approval_status ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:max_tolerated_dose ], + sh:order 0 ; + sh:path biolink:is_supplement ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -28257,78 +28209,103 @@ biolink:ProcessedMaterial a sh:NodeShape ; sh:order 14 ; sh:path biolink:iri ], [ sh:datatype xsd:boolean ; - sh:description "" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:is_toxic ], + sh:order 20 ; + sh:path biolink:deprecated ], + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_supplement ], + sh:order 10 ; + sh:path biolink:xref ], [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; sh:order 3 ; sh:path biolink:routes_of_delivery ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:category ] ; - sh:targetClass biolink:ProcessedMaterial . - -biolink:Protein a sh:NodeShape ; - sh:closed true ; - sh:description "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 19 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; + sh:order 13 ; sh:path biolink:id ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 5 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 6 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; + sh:order 4 ; + sh:path biolink:trade_name ] ; + sh:targetClass biolink:ProcessedMaterial . + +biolink:Protein a sh:NodeShape ; + sh:closed true ; + sh:description "A gene product that is composed of a chain of amino acid sequences and is produced by ribosome-mediated translation of mRNA" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -28336,38 +28313,61 @@ biolink:Protein a sh:NodeShape ; sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 0 ; + sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ], + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; @@ -28378,50 +28378,28 @@ biolink:ProteinDomain a sh:NodeShape ; sh:closed true ; sh:description "A conserved part of protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain. Protein domains maintain their structure and function independently of the proteins in which they are found. e.g. an SH3 domain." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:property [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], + sh:order 4 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -28434,61 +28412,82 @@ biolink:ProteinDomain a sh:NodeShape ; sh:order 13 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], + sh:order 11 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ] ; + sh:order 7 ; + sh:path biolink:id ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ] ; sh:targetClass biolink:ProteinDomain . biolink:ProteinFamily a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 12 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -28496,16 +28495,6 @@ biolink:ProteinFamily a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; @@ -28532,6 +28521,17 @@ biolink:ProteinFamily a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -28539,65 +28539,72 @@ biolink:ProteinFamily a sh:NodeShape ; sh:order 5 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 6 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:xref ] ; + sh:order 8 ; + sh:path biolink:iri ] ; sh:targetClass biolink:ProteinFamily . biolink:ProteinIsoform a sh:NodeShape ; sh:closed true ; sh:description "Represents a protein that is a specific isoform of the canonical or reference protein. See https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4114032/" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -28605,34 +28612,27 @@ biolink:ProteinIsoform a sh:NodeShape ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ] ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:ProteinIsoform . biolink:RNAProduct a sh:NodeShape ; @@ -28644,27 +28644,33 @@ biolink:RNAProduct a sh:NodeShape ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -28678,33 +28684,91 @@ biolink:RNAProduct a sh:NodeShape ; sh:order 8 ; sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ] ; + sh:targetClass biolink:RNAProduct . + +biolink:RNAProductIsoform a sh:NodeShape ; + sh:closed true ; + sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -28712,155 +28776,243 @@ biolink:RNAProduct a sh:NodeShape ; sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ] ; - sh:targetClass biolink:RNAProduct . - -biolink:RNAProductIsoform a sh:NodeShape ; - sh:closed true ; - sh:description "Represents a protein that is a specific isoform of the canonical or reference RNA" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; + sh:targetClass biolink:RNAProductIsoform . + +biolink:ReactionToCatalystAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 22 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 24 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 9 ; + sh:order 28 ; + sh:path biolink:subject_label_closure ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; + sh:maxCount 1 ; + sh:order 1 ; + sh:path biolink:reaction_direction ], + [ sh:datatype xsd:integer ; + sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:stoichiometry ], + [ sh:description "the side of a reaction being modeled (ie: left or right)" ; + sh:in ( "left" "right" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:reaction_side ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_evidence ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 37 ; sh:path rdf:type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:qualifiers ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; + sh:order 35 ; sh:path biolink:iri ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:object_namespace ], + [ sh:class biolink:GeneOrGeneProduct ; + sh:description "the chemical element that is the target of the statement" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:BlankNodeOrIRI ; sh:order 5 ; - sh:path biolink:full_name ], + sh:path rdf:object ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; + sh:order 36 ; sh:path biolink:category ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:p_value ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + sh:order 39 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 12 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 38 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:synonym ] ; - sh:targetClass biolink:RNAProductIsoform . - -biolink:ReactionToCatalystAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 23 ; + sh:path biolink:object_closure ], + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], + sh:order 3 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path rdf:predicate ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 32 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:p_value ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 40 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:integer ; - sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:stoichiometry ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:object_closure ], + sh:order 17 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -28874,92 +29026,50 @@ biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:knowledge_source ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 41 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 24 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:path biolink:negated ] ; + sh:targetClass biolink:ReactionToCatalystAssociation . + +biolink:ReactionToParticipantAssociation a sh:NodeShape ; + sh:closed true ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ], + sh:order 29 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdfs:label ], + sh:order 11 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:deprecated ], - [ sh:class biolink:GeneOrGeneProduct ; - sh:description "the chemical element that is the target of the statement" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 37 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:order 40 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -28967,94 +29077,28 @@ biolink:ReactionToCatalystAssociation a sh:NodeShape ; sh:order 21 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 22 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdf:type ], + sh:order 38 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], + sh:order 7 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_evidence ], [ sh:description "the side of a reaction being modeled (ie: left or right)" ; sh:in ( "left" "right" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:reaction_side ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path dct:description ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:subject_label_closure ] ; - sh:targetClass biolink:ReactionToCatalystAssociation . - -biolink:ReactionToParticipantAssociation a sh:NodeShape ; - sh:closed true ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:agent_type ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; @@ -29065,70 +29109,76 @@ biolink:ReactionToParticipantAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path biolink:category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdfs:label ], + sh:order 39 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_object ], + sh:order 35 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 18 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:publications ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 41 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:timepoint ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path rdf:type ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 32 ; + sh:path biolink:adjusted_p_value ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:minCount 1 ; + sh:order 14 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:MolecularEntity ; + sh:description "the chemical entity or entity that is an interactor" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path rdf:subject ], + [ sh:datatype xsd:integer ; + sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:stoichiometry ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:object_category_closure ], + sh:order 13 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -29142,107 +29192,92 @@ biolink:ReactionToParticipantAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:ChemicalEntity ; + sh:description "the chemical element that is the target of the statement" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path biolink:iri ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path rdf:object ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 33 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:retrieval_source_ids ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_evidence ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_namespace ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:p_value ], - [ sh:class biolink:ChemicalEntity ; - sh:description "the chemical element that is the target of the statement" ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path rdf:object ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 40 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:retrieval_source_ids ], + sh:order 8 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:knowledge_source ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 17 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 14 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:integer ; - sh:description "the relationship between the relative quantities of substances taking part in a reaction or forming a compound, typically a ratio of whole integers." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:stoichiometry ], - [ sh:description "the side of a reaction being modeled (ie: left or right)" ; - sh:in ( "left" "right" ) ; + sh:order 6 ; + sh:path biolink:negated ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:reaction_side ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_predicate ], + sh:order 34 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 26 ; + sh:path biolink:subject_namespace ], + [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; + sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 33 ; - sh:path biolink:has_supporting_studies ], + sh:order 1 ; + sh:path biolink:reaction_direction ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; @@ -29252,42 +29287,7 @@ biolink:ReactionToParticipantAssociation a sh:NodeShape ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 28 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:MolecularEntity ; - sh:description "the chemical entity or entity that is an interactor" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path rdf:subject ], - [ sh:description "the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)" ; - sh:in ( "left_to_right" "right_to_left" "bidirectional" "neutral" ) ; - sh:maxCount 1 ; - sh:order 1 ; - sh:path biolink:reaction_direction ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_subject ] ; + sh:path biolink:subject_label_closure ] ; sh:targetClass biolink:ReactionToParticipantAssociation . biolink:ReagentTargetedGene a sh:NodeShape ; @@ -29295,63 +29295,72 @@ biolink:ReagentTargetedGene a sh:NodeShape ; sh:description "A gene altered in its expression level in the context of some experiment as a result of being targeted by gene-knockdown reagent(s) such as a morpholino or RNAi." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -29359,19 +29368,10 @@ biolink:ReagentTargetedGene a sh:NodeShape ; sh:order 9 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -29385,60 +29385,29 @@ biolink:RegulatoryRegion a sh:NodeShape ; sh:description "A region (or regions) of the genome that contains known or putative regulatory elements that act in cis- or trans- to affect the transcription of gene" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:in_taxon_label ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -29446,33 +29415,64 @@ biolink:RegulatoryRegion a sh:NodeShape ; sh:order 12 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ] ; + sh:order 7 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:RegulatoryRegion . biolink:RelationshipQuantifier a sh:NodeShape ; sh:closed false ; - sh:ignoredProperties ( biolink:has_percentage biolink:has_quotient biolink:has_total biolink:has_count rdf:type ) ; + sh:ignoredProperties ( biolink:has_percentage rdf:type biolink:has_quotient biolink:has_total biolink:has_count ) ; sh:targetClass biolink:RelationshipQuantifier . biolink:RelationshipType a sh:NodeShape ; @@ -29492,94 +29492,94 @@ biolink:RelativeFrequencyAnalysisResult a sh:NodeShape ; sh:closed true ; sh:description "A result of a relative frequency analysis." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:date ; + sh:property [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:license ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 11 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ] ; + sh:order 9 ; + sh:path biolink:iri ] ; sh:targetClass biolink:RelativeFrequencyAnalysisResult . biolink:SensitivityQuantifier a sh:NodeShape ; @@ -29590,92 +29590,80 @@ biolink:SensitivityQuantifier a sh:NodeShape ; biolink:SequenceAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a sequence feature and a nucleic acid entity it is localized to." ; - sh:ignoredProperties ( biolink:end_interbase_coordinate biolink:phase biolink:genome_build rdf:type biolink:strand biolink:start_interbase_coordinate ) ; + sh:ignoredProperties ( rdf:type biolink:strand biolink:start_interbase_coordinate biolink:end_interbase_coordinate biolink:genome_build biolink:phase ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], + sh:order 13 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:float ; sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 29 ; sh:path biolink:adjusted_p_value ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 33 ; + sh:path biolink:category ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -29684,91 +29672,102 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:order 0 ; sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 11 ; sh:path biolink:knowledge_level ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:NamedThing ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; @@ -29776,44 +29775,45 @@ biolink:SequenceAssociation a sh:NodeShape ; sh:order 18 ; sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:NamedThing ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ] ; + sh:order 2 ; + sh:path rdf:object ] ; sh:targetClass biolink:SequenceAssociation . biolink:SequenceFeatureRelationship a sh:NodeShape ; @@ -29827,28 +29827,23 @@ biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -29856,130 +29851,77 @@ biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:order 36 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], + sh:order 33 ; + sh:path biolink:category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 31 ; + sh:path biolink:id ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:publications ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:NucleicAcidEntity ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -29988,357 +29930,398 @@ biolink:SequenceFeatureRelationship a sh:NodeShape ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:NucleicAcidEntity ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 28 ; + sh:path biolink:p_value ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ] ; - sh:targetClass biolink:SequenceFeatureRelationship . - -biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; - sh:closed false ; - sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 23 ; sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path rdfs:label ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:Treatment ; - sh:description "treatment whose efficacy is modulated by the subject variant" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:path biolink:subject_category ] ; + sh:targetClass biolink:SequenceFeatureRelationship . + +biolink:SequenceVariantModulatesTreatmentAssociation a sh:NodeShape ; + sh:closed false ; + sh:description "An association between a sequence variant and a treatment or health intervention. The treatment object itself encompasses both the disease and the drug used." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:SequenceVariant ; + sh:description "variant that modulates the treatment of some disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:SequenceVariant ; - sh:description "variant that modulates the treatment of some disease" ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Treatment ; + sh:description "treatment whose efficacy is modulated by the subject variant" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path rdf:predicate ] ; - sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . - -biolink:Serial a sh:NodeShape ; - sh:closed true ; - sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:mesh_terms ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:license ], + sh:order 36 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 24 ; - sh:path biolink:deprecated ], + sh:path biolink:object_namespace ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ] ; + sh:targetClass biolink:SequenceVariantModulatesTreatmentAssociation . + +biolink:Serial a sh:NodeShape ; + sh:closed true ; + sh:description "This class may rarely be instantiated except if use cases of a given knowledge graph support its utility." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:id ], + sh:order 12 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:iri ], + sh:order 0 ; + sh:path biolink:iso_abbreviation ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:synonym ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 23 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:summary ], [ sh:datatype xsd:string ; sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:pages ], - [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "volume of a book or music release in a collection/series or a published collection of journal issues in a serial publication" ; sh:maxCount 1 ; @@ -30346,43 +30329,48 @@ biolink:Serial a sh:NodeShape ; sh:order 1 ; sh:path biolink:volume ], [ sh:datatype xsd:string ; + sh:description "Serials (journals) should have industry-standard identifier such as from ISSN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:format ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:authors ], + sh:order 17 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:summary ], + sh:order 11 ; + sh:path biolink:rights ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 23 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:keywords ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 22 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:issue ], - [ sh:datatype xsd:string ; - sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -30390,11 +30378,17 @@ biolink:Serial a sh:NodeShape ; sh:order 15 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set, then the iso abbreviation pertains to the broader publication context (the journal) within which the given publication node is embedded, not the publication itself." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:iso_abbreviation ], + sh:order 18 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "issue of a newspaper, a scientific journal or magazine for reference purpose" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:issue ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -30402,44 +30396,49 @@ biolink:Serial a sh:NodeShape ; sh:order 13 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:rights ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 21 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Should generally be set to an ontology class defined term for 'serial' or 'journal'." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 20 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:category ] ; + sh:order 10 ; + sh:path biolink:license ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Serial . biolink:SeverityValue a sh:NodeShape ; sh:closed true ; sh:description "describes the severity of a phenotypic feature or disease" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -30447,15 +30446,26 @@ biolink:SeverityValue a sh:NodeShape ; sh:order 4 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -30463,27 +30473,22 @@ biolink:SeverityValue a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -30491,23 +30496,18 @@ biolink:SeverityValue a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ] ; + sh:order 12 ; + sh:path dct:description ] ; sh:targetClass biolink:SeverityValue . biolink:SiRNA a sh:NodeShape ; @@ -30515,67 +30515,61 @@ biolink:SiRNA a sh:NodeShape ; sh:description "A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. SRNAs trigger the cleavage of their target molecules." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -30583,15 +30577,21 @@ biolink:SiRNA a sh:NodeShape ; sh:order 5 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ] ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:SiRNA . biolink:SmallMolecule a sh:NodeShape ; @@ -30599,188 +30599,170 @@ biolink:SmallMolecule a sh:NodeShape ; sh:description "A small molecule entity is a molecular entity characterized by availability in small-molecule databases of SMILES, InChI, IUPAC, or other unambiguous representation of its precise chemical structure; for convenience of representation, any valid chemical representation is included, even if it is not strictly molecular (e.g., sodium ion)." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:trade_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_metabolite ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 16 ; sh:path biolink:has_attribute ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 2 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 2 ; - sh:path biolink:available_from ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_chemical_role ], + sh:order 12 ; + sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; - sh:path biolink:is_toxic ] ; - sh:targetClass biolink:SmallMolecule . - -biolink:Snv a sh:NodeShape ; - sh:closed true ; - sh:description "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], + sh:path biolink:is_toxic ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; + sh:order 17 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The state of the sequence w.r.t a reference sequence" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_biological_sequence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Gene ; - sh:description "Each allele can be associated with any number of genes" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene ], + sh:order 10 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; - sh:path rdf:type ], + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "indicates whether a molecular entity is a metabolite" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:is_metabolite ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; + sh:order 7 ; + sh:path biolink:xref ] ; + sh:targetClass biolink:SmallMolecule . + +biolink:Snv a sh:NodeShape ; + sh:closed true ; + sh:description "SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -30788,40 +30770,61 @@ biolink:Snv a sh:NodeShape ; sh:order 4 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:id ], + [ sh:class biolink:Gene ; + sh:description "Each allele can be associated with any number of genes" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene ], + [ sh:datatype xsd:string ; + sh:description "The state of the sequence w.r.t a reference sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ] ; + sh:order 1 ; + sh:path biolink:has_biological_sequence ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Snv . biolink:SocioeconomicExposure a sh:NodeShape ; sh:closed true ; sh:description "A socioeconomic exposure is a factor relating to social and financial status of an affected individual (e.g. poverty)." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:SocioeconomicAttribute ; - sh:description "connects any entity to an attribute" ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:timepoint ], - [ sh:class biolink:QuantityValue ; + sh:property [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:provided_by ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -30829,11 +30832,19 @@ biolink:SocioeconomicExposure a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_attribute_type ], + [ sh:class biolink:SocioeconomicAttribute ; + sh:description "connects any entity to an attribute" ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; @@ -30846,45 +30857,34 @@ biolink:SocioeconomicExposure a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 10 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:provided_by ], + sh:order 0 ; + sh:path biolink:timepoint ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path biolink:full_name ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -30908,50 +30908,46 @@ biolink:StudyPopulation a sh:NodeShape ; sh:closed true ; sh:description "A group of people banded together or treated as a group as participants in a research study." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -30959,28 +30955,32 @@ biolink:StudyPopulation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -30992,76 +30992,50 @@ biolink:StudyResult a sh:NodeShape ; sh:closed false ; sh:description "A collection of data items from a study that are about a particular study subject or experimental unit (the 'focus' of the Result) - optionally with context/provenance metadata that may be relevant to the interpretation of this data as evidence." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:format ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -31069,95 +31043,99 @@ biolink:StudyResult a sh:NodeShape ; sh:order 10 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ] ; - sh:targetClass biolink:StudyResult . - -biolink:StudyVariable a sh:NodeShape ; - sh:closed true ; - sh:description "a variable that is used as a measure in the investigation of a study" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], + sh:order 8 ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 6 ; + sh:path biolink:full_name ] ; + sh:targetClass biolink:StudyResult . + +biolink:StudyVariable a sh:NodeShape ; + sh:closed true ; + sh:description "a variable that is used as a measure in the investigation of a study" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -31169,11 +31147,33 @@ biolink:StudyVariable a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:StudyVariable . biolink:SubjectOfInvestigation a sh:NodeShape ; @@ -31185,29 +31185,29 @@ biolink:SubjectOfInvestigation a sh:NodeShape ; biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:property [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:float ; sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; @@ -31219,123 +31219,118 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 21 ; sh:path biolink:subject_category_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], [ sh:datatype xsd:anyURI ; sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:original_predicate ], - [ sh:class biolink:OrganismTaxon ; - sh:description "An association between individuals of different taxa." ; + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 31 ; + sh:path biolink:id ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 5 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -31343,59 +31338,53 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:class biolink:OrganismTaxon ; + sh:description "An association between individuals of different taxa." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 38 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -31407,7 +31396,18 @@ biolink:TaxonToTaxonAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:knowledge_source ] ; + sh:path biolink:knowledge_source ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:object_closure ] ; sh:targetClass biolink:TaxonToTaxonAssociation . biolink:TextMiningResult a sh:NodeShape ; @@ -31415,49 +31415,47 @@ biolink:TextMiningResult a sh:NodeShape ; sh:description "A result of text mining." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 13 ; + sh:path dct:description ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -31465,90 +31463,90 @@ biolink:TextMiningResult a sh:NodeShape ; sh:order 3 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ] ; + sh:order 1 ; + sh:path biolink:rights ] ; sh:targetClass biolink:TextMiningResult . biolink:ThingWithTaxon a sh:NodeShape ; sh:closed false ; sh:description "A mixin that can be used on any entity that can be taxonomically classified. This includes individual organisms; genes, their products and other molecular entities; body parts; biological processes" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:in_taxon_label ] ; + sh:path biolink:in_taxon_label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:ThingWithTaxon . biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:closed true ; sh:description "A gene is a collection of transcripts" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:property [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:class biolink:Transcript ; sh:description "connects an association to the subject of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -31556,198 +31554,200 @@ biolink:TranscriptToGeneRelationship a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 35 ; + sh:path rdfs:label ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; sh:order 12 ; sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:qualifier ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 1 ; + sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path rdf:type ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ] ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ] ; sh:targetClass biolink:TranscriptToGeneRelationship . biolink:TranscriptionFactorBindingSite a sh:NodeShape ; @@ -31755,22 +31755,16 @@ biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:description "A region (or regions) of the genome that contains a region of DNA known or predicted to bind a protein that modulates gene transcription" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 10 ; @@ -31781,36 +31775,29 @@ biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -31818,237 +31805,261 @@ biolink:TranscriptionFactorBindingSite a sh:NodeShape ; sh:order 3 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:in_taxon ] ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:id ] ; sh:targetClass biolink:TranscriptionFactorBindingSite . biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:property [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:nodeKind sh:IRI ; + sh:order 44 ; + sh:path biolink:disease_context_qualifier ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "The relationship to the disease" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], + sh:order 31 ; + sh:path biolink:id ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 25 ; sh:path biolink:subject_label_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 45 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:Disease ; + sh:description "disease" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], + sh:order 2 ; + sh:path rdf:object ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; sh:order 33 ; sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 44 ; - sh:path biolink:disease_context_qualifier ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], + sh:order 18 ; + sh:path biolink:object_category ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 39 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], + sh:order 35 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:order 43 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], - [ sh:class biolink:SequenceVariant ; - sh:description "A variant that has a role in modeling the disease." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; + sh:order 32 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], + sh:order 36 ; + sh:path dct:description ], [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 22 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 39 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], + sh:order 26 ; + sh:path biolink:object_label_closure ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 37 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], + sh:order 16 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Disease ; - sh:description "disease" ; + sh:order 20 ; + sh:path biolink:object_closure ], + [ sh:class biolink:SequenceVariant ; + sh:description "A variant that has a role in modeling the disease." ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "The relationship to the disease" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; @@ -32056,120 +32067,135 @@ biolink:VariantAsAModelOfDiseaseAssociation a sh:NodeShape ; sh:order 8 ; sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], + sh:order 14 ; + sh:path biolink:original_subject ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 24 ; + sh:path biolink:object_namespace ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 27 ; sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ] ; + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ] ; sh:targetClass biolink:VariantAsAModelOfDiseaseAssociation . biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:property [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:negated ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 20 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:order 40 ; - sh:path biolink:subject_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 44 ; - sh:path biolink:disease_context_qualifier ], + sh:order 40 ; + sh:path biolink:subject_direction_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:subject_category ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 36 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -32177,112 +32203,84 @@ biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 31 ; sh:path biolink:id ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path dct:description ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:order 33 ; + sh:path biolink:category ], + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 30 ; - sh:path biolink:has_supporting_studies ], + sh:order 44 ; + sh:path biolink:disease_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; - sh:maxCount 1 ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:qualified_predicate ], + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 42 ; + sh:path biolink:object_direction_qualifier ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 32 ; + sh:path biolink:iri ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 18 ; sh:path biolink:object_category ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], - [ sh:class biolink:Disease ; - sh:description "a disease that is associated with that variant" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the disease state" ; - sh:maxCount 1 ; - sh:minCount 1 ; + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:order 7 ; + sh:path biolink:has_evidence ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:object_category_closure ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 45 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 3 ; + sh:path biolink:negated ], + [ sh:datatype xsd:string ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], + sh:order 43 ; + sh:path biolink:qualified_predicate ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; @@ -32290,109 +32288,111 @@ biolink:VariantToDiseaseAssociation a sh:NodeShape ; sh:order 14 ; sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "E.g. is pathogenic for" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path rdf:type ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 35 ; + sh:path rdfs:label ], + [ sh:class biolink:Disease ; + sh:description "a disease that is associated with that variant" ; sh:maxCount 1 ; - sh:order 42 ; - sh:path biolink:object_direction_qualifier ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 15 ; + sh:path biolink:original_predicate ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:object_closure ], + sh:order 34 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path biolink:subject_aspect_qualifier ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], + sh:order 45 ; + sh:path biolink:frequency_qualifier ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 41 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; + sh:order 30 ; + sh:path biolink:has_supporting_studies ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 7 ; - sh:path biolink:has_evidence ], + sh:order 6 ; + sh:path biolink:publications ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 5 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:description "E.g. is pathogenic for" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ] ; + sh:order 1 ; + sh:path rdf:predicate ] ; sh:targetClass biolink:VariantToDiseaseAssociation . biolink:VariantToEntityAssociationMixin a sh:NodeShape ; sh:closed false ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:class biolink:SequenceVariant ; + sh:property [ sh:class biolink:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path rdf:subject ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], [ sh:class biolink:NamedThing ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -32405,133 +32405,88 @@ biolink:VariantToEntityAssociationMixin a sh:NodeShape ; biolink:VariantToGeneAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and a gene, where the variant has a genetic association with the gene (i.e. is in linkage disequilibrium)" ; - sh:ignoredProperties ( biolink:stage_qualifier biolink:expression_site biolink:phenotypic_state rdf:type biolink:quantifier_qualifier ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_object ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated with some other entity" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:ignoredProperties ( rdf:type biolink:stage_qualifier biolink:quantifier_qualifier biolink:expression_site biolink:phenotypic_state ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:object_category ], + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_namespace ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:order 24 ; + sh:path biolink:object_namespace ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:object_label_closure ], + sh:minCount 1 ; + sh:order 11 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:subject_label_closure ], + sh:order 9 ; + sh:path biolink:primary_knowledge_source ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category_closure ], + sh:order 22 ; + sh:path biolink:object_category_closure ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 36 ; sh:path dct:description ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category_closure ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 6 ; + sh:path biolink:publications ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:adjusted_p_value ], + sh:order 38 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdfs:label ], + sh:order 8 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:agent_type ], + sh:nodeKind sh:Literal ; + sh:order 31 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:iri ], + sh:order 4 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; + sh:order 25 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:timepoint ], + sh:order 14 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:qualifier ], + sh:order 10 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:Gene ; sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; @@ -32539,46 +32494,101 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path rdf:object ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:id ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:order 28 ; + sh:path biolink:p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 11 ; - sh:path biolink:knowledge_level ], + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:knowledge_source ], + sh:order 35 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 23 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated with some other entity" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 21 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 34 ; sh:path rdf:type ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path biolink:publications ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 37 ; + sh:path biolink:has_attribute ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:agent_type ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:subject_category ], + sh:order 5 ; + sh:path biolink:qualifiers ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:subject_closure ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:category ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; sh:order 30 ; sh:path biolink:has_supporting_studies ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:boolean ; sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; @@ -32590,34 +32600,6 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:object_closure ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 37 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:qualifiers ], [ sh:class biolink:EvidenceType ; sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; @@ -32628,29 +32610,42 @@ biolink:VariantToGeneAssociation a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; - sh:path biolink:original_predicate ] ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:string ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:original_object ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 26 ; + sh:path biolink:object_label_closure ] ; sh:targetClass biolink:VariantToGeneAssociation . biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:closed true ; sh:description "An association between a variant and expression of a gene (i.e. e-QTL)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:agent_type ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:retrieval_source_ids ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:Literal ; + sh:order 19 ; + sh:path biolink:original_predicate ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 34 ; - sh:path biolink:has_supporting_studies ], + sh:order 11 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -32659,99 +32654,92 @@ biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:order 5 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path dct:description ], + sh:order 36 ; + sh:path biolink:iri ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:object_category_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:agent_type ], + [ sh:class biolink:Gene ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 6 ; + sh:path rdf:object ], + [ sh:class biolink:DiseaseOrPhenotypicFeature ; + sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:phenotypic_state ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 27 ; + sh:path biolink:subject_namespace ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 9 ; sh:path biolink:qualifiers ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 15 ; - sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path rdfs:label ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:p_value ], + [ sh:datatype xsd:string ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_object ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Optional quantitative value indicating degree of expression." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 21 ; - sh:path biolink:subject_category ], - [ sh:class biolink:Publication ; - sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:publications ], + sh:order 0 ; + sh:path biolink:quantifier_qualifier ], [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 25 ; - sh:path biolink:subject_category_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:category ], + sh:order 22 ; + sh:path biolink:object_category ], [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 42 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:negated ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 30 ; sh:path biolink:object_label_closure ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:qualifier ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 41 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path biolink:original_predicate ], - [ sh:class biolink:AnatomicalEntity ; - sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:expression_site ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 23 ; - sh:path biolink:subject_closure ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:object_category_closure ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; @@ -32759,23 +32747,16 @@ biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:order 17 ; sh:path biolink:timepoint ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:original_subject ], - [ sh:class biolink:Gene ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 24 ; + sh:path biolink:object_closure ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 6 ; - sh:path rdf:object ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; sh:nodeKind sh:IRI ; - sh:order 11 ; - sh:path biolink:has_evidence ], + sh:order 21 ; + sh:path biolink:subject_category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -32783,17 +32764,38 @@ biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 35 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 27 ; - sh:path biolink:subject_namespace ], + sh:order 33 ; + sh:path biolink:adjusted_p_value ], [ sh:datatype xsd:string ; sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:class biolink:Publication ; + sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:nodeKind sh:Literal ; + sh:order 38 ; + sh:path rdf:type ], + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; + sh:order 31 ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:string ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:qualifier ], [ sh:class biolink:SequenceVariant ; sh:description "a sequence variant in which the allele state is associated with some other entity" ; sh:maxCount 1 ; @@ -32801,320 +32803,249 @@ biolink:VariantToGeneExpressionAssociation a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + [ sh:datatype xsd:string ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:p_value ], - [ sh:class biolink:DiseaseOrPhenotypicFeature ; - sh:description "in experiments (e.g. gene expression) assaying diseased or unhealthy tissue, the phenotypic state can be put here, e.g. MONDO ID. For healthy tissues, use XXX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:phenotypic_state ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:order 28 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:string ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:negated ], - [ sh:class biolink:OntologyClass ; - sh:description "Optional quantitative value indicating degree of expression." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:quantifier_qualifier ], + sh:order 12 ; + sh:path biolink:knowledge_source ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 28 ; - sh:path biolink:object_namespace ], + sh:order 40 ; + sh:path dct:description ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:knowledge_level ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 34 ; + sh:path biolink:has_supporting_studies ], [ sh:class biolink:LifeStage ; sh:description "stage during which gene or protein expression of takes place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:stage_qualifier ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:adjusted_p_value ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 25 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 38 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; - sh:maxCount 1 ; + sh:order 23 ; + sh:path biolink:subject_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:knowledge_source ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 37 ; + sh:path biolink:category ], + [ sh:class biolink:AnatomicalEntity ; + sh:description "location in which gene or protein expression takes place. May be cell, tissue, or organ." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:object_category ], + sh:order 1 ; + sh:path biolink:expression_site ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 42 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:object_closure ] ; + sh:order 18 ; + sh:path biolink:original_subject ] ; sh:targetClass biolink:VariantToGeneExpressionAssociation . biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; + sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_namespace ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 35 ; + sh:path rdf:type ], + [ sh:class biolink:BiologicalSex ; + sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; sh:maxCount 1 ; - sh:order 47 ; - sh:path biolink:object_direction_qualifier ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 38 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:integer ; - sh:description "total number of things in a particular reference set" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path biolink:has_total ], - [ sh:class biolink:PhenotypicFeature ; - sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; + sh:order 3 ; + sh:path biolink:sex_qualifier ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 19 ; + sh:path biolink:object_category ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 46 ; - sh:path biolink:object_aspect_qualifier ], + sh:order 25 ; + sh:path biolink:object_namespace ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 26 ; - sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:original_predicate ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:negated ], + sh:order 48 ; + sh:path biolink:qualified_predicate ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:object_category_closure ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:object_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:subject_closure ], - [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:primary_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:p_value ], [ sh:datatype xsd:double ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 42 ; sh:path biolink:has_quotient ], - [ sh:datatype xsd:time ; - sh:description "a point in time" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:timepoint ], - [ sh:class biolink:SequenceVariant ; - sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:class biolink:BiologicalSex ; - sh:description "a qualifier used in a phenotypic association to state whether the association is specific to a particular sex." ; + [ sh:class biolink:Disease ; + sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:sex_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:order 49 ; + sh:path biolink:disease_context_qualifier ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; - sh:order 45 ; - sh:path biolink:subject_direction_qualifier ], + sh:order 47 ; + sh:path biolink:object_direction_qualifier ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 12 ; + sh:path biolink:knowledge_level ], [ sh:class biolink:OntologyClass ; sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; sh:nodeKind sh:IRI ; sh:order 6 ; sh:path biolink:qualifiers ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path rdfs:label ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 38 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:integer ; + sh:description "number of things with a particular property" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 50 ; - sh:path biolink:frequency_qualifier ], - [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:order 40 ; + sh:path biolink:has_count ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:qualifier ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 8 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:RetrievalSource ; - sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; - sh:nodeKind sh:IRI ; - sh:order 28 ; - sh:path biolink:retrieval_source_ids ], + sh:order 43 ; + sh:path biolink:has_percentage ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 7 ; sh:path biolink:publications ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 8 ; + sh:path biolink:has_evidence ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:original_object ], - [ sh:datatype xsd:integer ; - sh:description "number of things with a particular property" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path biolink:has_count ], + sh:order 36 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path rdf:predicate ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 9 ; + sh:path biolink:knowledge_source ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:subject_category ], + [ sh:datatype xsd:integer ; + sh:description "total number of things in a particular reference set" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 30 ; - sh:path biolink:adjusted_p_value ], + sh:order 41 ; + sh:path biolink:has_total ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 44 ; - sh:path biolink:subject_aspect_qualifier ], - [ sh:class biolink:Disease ; - sh:description "A context qualifier representing a disease or condition in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 49 ; - sh:path biolink:disease_context_qualifier ], + sh:order 24 ; + sh:path biolink:subject_namespace ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 32 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:knowledge_source ], + sh:order 17 ; + sh:path biolink:original_object ], [ sh:datatype xsd:string ; sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; sh:order 27 ; sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; - sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; + sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 48 ; - sh:path biolink:qualified_predicate ], + sh:order 1 ; + sh:path rdf:predicate ], + [ sh:datatype xsd:string ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 44 ; + sh:path biolink:subject_aspect_qualifier ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:IRI ; sh:order 22 ; sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; + sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 35 ; - sh:path rdf:type ], + sh:order 15 ; + sh:path biolink:original_subject ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -33122,35 +33053,10 @@ biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 37 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:original_subject ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; - sh:maxCount 1 ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 43 ; - sh:path biolink:has_percentage ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:subject_category ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:object_category ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 12 ; - sh:path biolink:knowledge_level ], + sh:order 21 ; + sh:path biolink:object_closure ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -33162,6 +33068,12 @@ biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:aggregator_knowledge_source ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:adjusted_p_value ], [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; sh:maxCount 1 ; @@ -33169,227 +33081,279 @@ biolink:VariantToPhenotypicFeatureAssociation a sh:NodeShape ; sh:order 13 ; sh:path biolink:agent_type ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_namespace ], - [ sh:class biolink:Study ; - sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; - sh:nodeKind sh:IRI ; - sh:order 31 ; - sh:path biolink:has_supporting_studies ] ; - sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . - -biolink:VariantToPopulationAssociation a sh:NodeShape ; - sh:closed true ; - sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:order 46 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 33 ; + sh:path biolink:iri ], + [ sh:datatype xsd:time ; + sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:timepoint ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; sh:order 20 ; - sh:path biolink:original_predicate ], + sh:path biolink:subject_closure ], + [ sh:datatype xsd:string ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:primary_knowledge_source ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 32 ; + sh:path biolink:id ], + [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 45 ; + sh:path biolink:subject_direction_qualifier ], + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:negated ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:p_value ], [ sh:class biolink:Study ; sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; sh:nodeKind sh:IRI ; - sh:order 35 ; + sh:order 31 ; sh:path biolink:has_supporting_studies ], [ sh:datatype xsd:string ; sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 30 ; + sh:order 26 ; sh:path biolink:subject_label_closure ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; + [ sh:class biolink:RetrievalSource ; + sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; + sh:nodeKind sh:IRI ; sh:order 28 ; - sh:path biolink:subject_namespace ], - [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; - sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:path biolink:retrieval_source_ids ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 17 ; - sh:path biolink:agent_type ], - [ sh:datatype xsd:string ; - sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:aggregator_knowledge_source ], - [ sh:datatype xsd:float ; - sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:order 16 ; + sh:path biolink:original_predicate ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 34 ; - sh:path biolink:adjusted_p_value ], + sh:order 50 ; + sh:path biolink:frequency_qualifier ], + [ sh:class biolink:SequenceVariant ; + sh:description "a sequence variant in which the allele state is associated in some way with the phenotype state" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 38 ; + sh:order 34 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; + [ sh:class biolink:PhenotypicFeature ; + sh:description "connects an association to the object of the association. For example, in a gene-to-phenotype association, the gene is subject and phenotype is object." ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:knowledge_source ], + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ] ; + sh:targetClass biolink:VariantToPhenotypicFeatureAssociation . + +biolink:VariantToPopulationAssociation a sh:NodeShape ; + sh:closed true ; + sh:description "An association between a variant and a population, where the variant has particular frequency in the population" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:class biolink:SequenceVariant ; + sh:description "an allele that has a certain frequency in a given population" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path rdf:subject ], + [ sh:class biolink:EvidenceType ; + sh:description "connects an association to an instance of supporting evidence" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_evidence ], + [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; + sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 16 ; + sh:path biolink:knowledge_level ], [ sh:datatype xsd:string ; sh:description "used to hold the original subject of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 19 ; sh:path biolink:original_subject ], - [ sh:datatype xsd:boolean ; - sh:description "if set to true, then the association is negated i.e. is not true" ; + [ sh:datatype xsd:integer ; + sh:description "number all populations that carry a particular allele, aka allele number" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:negated ], - [ sh:class biolink:PopulationOfIndividualOrganisms ; - sh:description "the population that is observed to have the frequency" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path rdf:object ], + sh:order 4 ; + sh:path biolink:has_total ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path biolink:timepoint ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:qualifiers ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An Information Resource from which the knowledge expressed in an Association was retrieved, directly or indirectly. This can be any resource through which the knowledge passed on its way to its currently serialized form. In practice, implementers should use one of the more specific subtypes of this generic property." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 40 ; - sh:path rdfs:label ], - [ sh:description "Describes the level of knowledge expressed in a statement, based on the reasoning or analysis methods used to generate the statement, or the scope or specificity of what the statement expresses to be true." ; - sh:in ( "knowledge_assertion" "logical_entailment" "prediction" "statistical_association" "observation" "not_provided" ) ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:order 16 ; - sh:path biolink:knowledge_level ], - [ sh:class biolink:SequenceVariant ; - sh:description "an allele that has a certain frequency in a given population" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path rdf:subject ], - [ sh:datatype xsd:string ; - sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:order 13 ; + sh:path biolink:knowledge_source ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:nodeKind sh:Literal ; - sh:order 25 ; - sh:path biolink:object_closure ], + sh:order 38 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 42 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 26 ; + sh:path biolink:subject_category_closure ], [ sh:datatype xsd:string ; - sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 24 ; - sh:path biolink:subject_closure ], + sh:order 14 ; + sh:path biolink:primary_knowledge_source ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "An intermediate aggregator resource from which knowledge expressed in an Association was retrieved downstream of the original source, on its path to its current serialized form." ; sh:nodeKind sh:Literal ; - sh:order 41 ; - sh:path dct:description ], + sh:order 15 ; + sh:path biolink:aggregator_knowledge_source ], [ sh:class biolink:OntologyClass ; sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:maxCount 1 ; sh:nodeKind sh:IRI ; sh:order 23 ; sh:path biolink:object_category ], - [ sh:datatype xsd:integer ; - sh:description "number all populations that carry a particular allele, aka allele number" ; + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:has_total ], - [ sh:datatype xsd:double ; - sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; + sh:order 37 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:has_quotient ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 27 ; - sh:path biolink:object_category_closure ], + sh:order 40 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:description "Used to hold the subject label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 30 ; + sh:path biolink:subject_label_closure ], + [ sh:datatype xsd:float ; + sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:qualifier ], + sh:order 33 ; + sh:path biolink:p_value ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 29 ; - sh:path biolink:object_namespace ], + sh:order 21 ; + sh:path biolink:original_object ], [ sh:class biolink:RetrievalSource ; sh:description "A list of retrieval sources that served as a source of knowledge expressed in an Edge, or a source of data used to generate this knowledge." ; sh:nodeKind sh:IRI ; sh:order 32 ; sh:path biolink:retrieval_source_ids ], - [ sh:datatype xsd:integer ; - sh:description "number in object population that carry a particular allele, aka allele count" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:has_count ], - [ sh:datatype ; - sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + [ sh:datatype xsd:boolean ; + sh:description "if set to true, then the association is negated i.e. is not true" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:frequency_qualifier ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the subject category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:nodeKind sh:IRI ; - sh:order 26 ; - sh:path biolink:subject_category_closure ], - [ sh:class biolink:EvidenceType ; - sh:description "connects an association to an instance of supporting evidence" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_evidence ], - [ sh:class biolink:OntologyClass ; - sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 22 ; - sh:path biolink:subject_category ], + sh:order 8 ; + sh:path biolink:negated ], [ sh:class biolink:Publication ; sh:description "One or more publications that report the statement expressed in an Association, or provide information used as evidence supporting this statement." ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:publications ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 24 ; + sh:path biolink:subject_closure ], + [ sh:description "Describes the high-level category of agent who originally generated a statement of knowledge or other type of information." ; + sh:in ( "manual_agent" "automated_agent" "data_analysis_pipeline" "computational_model" "text_mining_agent" "image_processing_agent" "manual_validation_of_automated_agent" "not_provided" ) ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:order 17 ; + sh:path biolink:agent_type ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the subject namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 28 ; + sh:path biolink:subject_namespace ], + [ sh:datatype xsd:string ; + sh:description "Used to hold the object closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:Literal ; + sh:order 25 ; + sh:path biolink:object_closure ], + [ sh:datatype xsd:integer ; + sh:description "number in object population that carry a particular allele, aka allele count" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:has_count ], [ sh:datatype xsd:string ; sh:description "rdf:type of biolink:Association should be fixed at rdf:Statement" ; sh:nodeKind sh:Literal ; sh:order 39 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "used to hold the original object of a relation (or predicate) that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:original_object ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an association to qualifiers that modify or qualify the meaning of that association" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:qualifiers ], + sh:order 36 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The most upstream source of the knowledge expressed in an Association that an implementer can identify. Performing a rigorous analysis of upstream data providers is expected; every effort is made to catalog the most upstream source of data in this property. Only one data source should be declared primary in any association. \"aggregator knowledge source\" can be used to capture non-primary sources." ; - sh:maxCount 1 ; + sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:primary_knowledge_source ], + sh:order 31 ; + sh:path biolink:object_label_closure ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -33398,64 +33362,93 @@ biolink:VariantToPopulationAssociation a sh:NodeShape ; sh:order 1 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 37 ; - sh:path biolink:iri ], - [ sh:datatype xsd:float ; - sh:description "A quantitative confidence value that represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 33 ; - sh:path biolink:p_value ], - [ sh:datatype xsd:double ; - sh:description "equivalent to has quotient multiplied by 100" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:has_percentage ], + sh:order 41 ; + sh:path dct:description ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 43 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 42 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Used to hold the object label closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:description "grouping slot for all qualifiers on an edge. useful for testing compliance with association classes" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 31 ; - sh:path biolink:object_label_closure ], + sh:order 9 ; + sh:path biolink:qualifier ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "Used to hold the object namespace of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 29 ; + sh:path biolink:object_namespace ], + [ sh:datatype xsd:double ; + sh:description "frequency of allele in population, expressed as a number with allele divided by number in reference population, aka allele frequency" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:has_quotient ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the object category closure of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:nodeKind sh:IRI ; + sh:order 27 ; + sh:path biolink:object_category_closure ], + [ sh:datatype xsd:anyURI ; + sh:description "used to hold the original relation/predicate that an external knowledge source uses before transformation to match the biolink-model specification." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 20 ; + sh:path biolink:original_predicate ], + [ sh:datatype xsd:float ; + sh:description "The adjusted p-value is the probability of obtaining test results at least as extreme as the results actually observed, under the assumption that the null hypothesis is correct, adjusted for multiple comparisons. P is always italicized and capitalized. The actual P value* should be expressed (P=. 04) rather than expressing a statement of inequality (P<. 05), unless P<." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 34 ; + sh:path biolink:adjusted_p_value ], + [ sh:class biolink:PopulationOfIndividualOrganisms ; + sh:description "the population that is observed to have the frequency" ; sh:maxCount 1 ; sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path rdf:object ], + [ sh:class biolink:OntologyClass ; + sh:description "Used to hold the biolink class/category of an association. This is a denormalized field used primarily in the SQL serialization of a knowledge graph via KGX." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 22 ; + sh:path biolink:subject_category ], + [ sh:datatype ; + sh:description "a qualifier used in a phenotypic association to state how frequent the phenotype is observed in the subject" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 36 ; - sh:path biolink:id ] ; + sh:order 7 ; + sh:path biolink:frequency_qualifier ], + [ sh:datatype xsd:double ; + sh:description "equivalent to has quotient multiplied by 100" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:has_percentage ], + [ sh:class biolink:Study ; + sh:description "A study that produced information used as evidence to generate the knowledge expressed in an Association." ; + sh:nodeKind sh:IRI ; + sh:order 35 ; + sh:path biolink:has_supporting_studies ] ; sh:targetClass biolink:VariantToPopulationAssociation . biolink:Vertebrate a sh:NodeShape ; sh:closed true ; sh:description "A sub-phylum of animals consisting of those having a bony or cartilaginous vertebral column." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -33463,60 +33456,67 @@ biolink:Vertebrate a sh:NodeShape ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 6 ; + sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; @@ -33529,22 +33529,16 @@ biolink:Virus a sh:NodeShape ; sh:description "A virus is a microorganism that replicates itself as a microRNA and infects the host cell." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -33552,60 +33546,66 @@ biolink:Virus a sh:NodeShape ; sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ] ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:Virus . biolink:WebPage a sh:NodeShape ; @@ -33613,37 +33613,49 @@ biolink:WebPage a sh:NodeShape ; sh:description "a document that is published according to World Wide Web standards, which may incorporate text, graphics, sound, and/or other features." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 11 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdf:type ], + sh:order 9 ; + sh:path biolink:format ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], + sh:order 15 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:description "executive summary of a publication" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 2 ; + sh:path biolink:summary ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -33651,20 +33663,20 @@ biolink:WebPage a sh:NodeShape ; sh:order 16 ; sh:path biolink:category ], [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 18 ; + sh:path rdfs:label ], [ sh:class biolink:Agent ; sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:authors ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 17 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -33682,104 +33694,82 @@ biolink:WebPage a sh:NodeShape ; sh:order 13 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:id ], + sh:order 7 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:order 8 ; + sh:path biolink:rights ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], + sh:order 4 ; + sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], + sh:order 19 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 20 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; + [ sh:datatype xsd:string ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], + sh:order 6 ; + sh:path dct:type ], [ sh:datatype xsd:string ; - sh:description "executive summary of a publication" ; + sh:description "Different kinds of publication subtypes will have different preferred identifiers (curies when feasible). Precedence of identifiers for scientific articles is as follows: PMID if available; DOI if not; actual alternate CURIE otherwise. Enclosing publications (i.e. referenced by 'published in' node property) such as books and journals, should have industry-standard identifier such as from ISBN and ISSN." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:summary ] ; + sh:order 14 ; + sh:path biolink:id ] ; sh:targetClass biolink:WebPage . biolink:Behavior a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:in_taxon_label ], + sh:order 0 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -33787,73 +33777,91 @@ biolink:Behavior a sh:NodeShape ; sh:order 10 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ] ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Behavior . biolink:BehavioralFeature a sh:NodeShape ; sh:closed true ; sh:description "A phenotypic feature which is behavioral in nature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -33861,27 +33869,18 @@ biolink:BehavioralFeature a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; @@ -33889,43 +33888,43 @@ biolink:BehavioralFeature a sh:NodeShape ; sh:order 1 ; sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ] ; + sh:order 5 ; + sh:path biolink:synonym ] ; sh:targetClass biolink:BehavioralFeature . biolink:CellularComponent a sh:NodeShape ; sh:closed true ; sh:description "A location in or around a cell" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:property [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -33934,49 +33933,47 @@ biolink:CellularComponent a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -33984,27 +33981,41 @@ biolink:CellularComponent a sh:NodeShape ; sh:order 7 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ] ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ] ; sh:targetClass biolink:CellularComponent . biolink:ClinicalAttribute a sh:NodeShape ; sh:closed true ; sh:description "Attributes relating to a clinical manifestation" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; @@ -34016,40 +34027,44 @@ biolink:ClinicalAttribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34057,86 +34072,79 @@ biolink:ClinicalAttribute a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ] ; + sh:targetClass biolink:ClinicalAttribute . + +biolink:Dataset a sh:NodeShape ; + sh:closed true ; + sh:description "an item that refers to a collection of data from a data source." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], + sh:order 1 ; + sh:path biolink:rights ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; + sh:order 13 ; sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 13 ; + sh:order 14 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ] ; - sh:targetClass biolink:ClinicalAttribute . - -biolink:Dataset a sh:NodeShape ; - sh:closed true ; - sh:description "an item that refers to a collection of data from a data source." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:full_name ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 4 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 12 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -34144,22 +34152,26 @@ biolink:Dataset a sh:NodeShape ; sh:order 15 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], + sh:order 0 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34168,21 +34180,9 @@ biolink:Dataset a sh:NodeShape ; sh:order 8 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ] ; + sh:order 11 ; + sh:path rdf:type ] ; sh:targetClass biolink:Dataset . biolink:DatasetDistribution a sh:NodeShape ; @@ -34190,28 +34190,33 @@ biolink:DatasetDistribution a sh:NodeShape ; sh:description "an item that holds distribution level information about a dataset." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:license ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:creation_date ], + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -34221,67 +34226,62 @@ biolink:DatasetDistribution a sh:NodeShape ; [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:rights ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], + sh:order 1 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:order 3 ; + sh:path biolink:format ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:distribution_download_url ], + sh:order 2 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], + sh:order 0 ; + sh:path biolink:distribution_download_url ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:format ] ; + sh:order 9 ; + sh:path biolink:id ] ; sh:targetClass biolink:DatasetDistribution . biolink:Device a sh:NodeShape ; @@ -34289,42 +34289,16 @@ biolink:Device a sh:NodeShape ; sh:description "A thing made or adapted for a particular purpose, especially a piece of mechanical or electronic equipment" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34332,23 +34306,49 @@ biolink:Device a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -34362,179 +34362,184 @@ biolink:Exon a sh:NodeShape ; sh:description "A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:order 10 ; + sh:path rdfs:label ] ; sh:targetClass biolink:Exon . biolink:GeneFamily a sh:NodeShape ; sh:closed true ; sh:description "any grouping of multiple genes or gene products related by common descent" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Gene ; - sh:description "connects an entity with one or more gene or gene products" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_gene_or_gene_product ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdf:type ], + sh:order 6 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:order 8 ; + sh:path biolink:iri ], + [ sh:class biolink:Gene ; + sh:description "connects an entity with one or more gene or gene products" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_gene_or_gene_product ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:synonym ] ; + sh:order 14 ; + sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:GeneFamily . biolink:GeneProductMixin a sh:NodeShape ; sh:closed false ; sh:description "The functional molecular product of a single gene locus. Gene products are either proteins or functional RNA molecules." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 0 ; @@ -34544,12 +34549,7 @@ biolink:GeneProductMixin a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:GeneProductMixin . biolink:GeneticInheritance a sh:NodeShape ; @@ -34557,56 +34557,60 @@ biolink:GeneticInheritance a sh:NodeShape ; sh:description "The pattern or 'mode' in which a particular genetic trait or disorder is passed from one generation to the next, e.g. autosomal dominant, autosomal recessive, etc." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -34614,55 +34618,82 @@ biolink:GeneticInheritance a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ] ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:GeneticInheritance . biolink:InformationContentEntity a sh:NodeShape ; sh:closed false ; sh:description "a piece of information that typically describes some topic of discourse or is used as support." ; - sh:ignoredProperties ( dct:type biolink:upstream_resource_ids biolink:summary dct:distribution biolink:source_web_page biolink:resource_role biolink:mesh_terms biolink:distribution_download_url biolink:authors biolink:resource_id biolink:published_in biolink:chapter schema1:logo biolink:keywords biolink:volume biolink:ingest_date biolink:iso_abbreviation biolink:has_dataset rdf:type biolink:pages biolink:issue ) ; + sh:ignoredProperties ( biolink:iso_abbreviation biolink:chapter biolink:summary biolink:source_web_page biolink:ingest_date dct:distribution rdf:type biolink:upstream_resource_ids biolink:volume biolink:issue biolink:has_dataset dct:type biolink:resource_id biolink:mesh_terms biolink:pages schema1:logo biolink:published_in biolink:distribution_download_url biolink:resource_role biolink:keywords biolink:authors ) ; sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:creation_date ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 2 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -34675,17 +34706,15 @@ biolink:InformationContentEntity a sh:NodeShape ; sh:order 13 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -34693,101 +34722,77 @@ biolink:InformationContentEntity a sh:NodeShape ; sh:order 9 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:creation_date ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ] ; + sh:order 8 ; + sh:path biolink:id ] ; sh:targetClass biolink:InformationContentEntity . biolink:Onset a sh:NodeShape ; sh:closed true ; sh:description "The age group in which (disease) symptom manifestations appear." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:class biolink:Attribute ; + sh:property [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 13 ; sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; @@ -34799,126 +34804,142 @@ biolink:Onset a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ] ; + sh:order 14 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Onset . biolink:OrganismalEntity a sh:NodeShape ; sh:closed false ; sh:description "A named entity that is either a part of an organism, a whole organism, population or clade of organisms, excluding chemical entities" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:order 11 ; + sh:path dct:description ] ; sh:targetClass biolink:OrganismalEntity . biolink:PredicateMapping a sh:NodeShape ; sh:closed true ; sh:description "A deprecated predicate mapping object contains the deprecated predicate and an example of the rewiring that should be done to use a qualified statement in its place." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:NamedThing ; + sh:property [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; + sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:maxCount 1 ; + sh:order 10 ; + sh:path biolink:object_direction_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; + sh:nodeKind sh:IRI ; + sh:order 18 ; + sh:path biolink:exact_match ], + [ sh:class biolink:NamedThing ; sh:description "a list of terms from different schemas or terminology systems that have a narrower, more specific meaning. Narrower terms are typically shown as children in a hierarchy or tree." ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:narrow_match ], - [ sh:datatype xsd:string ; + [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; + sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:subject_context_qualifier ], + sh:order 15 ; + sh:path biolink:causal_mechanism_qualifier ], + [ sh:class biolink:OrganismTaxon ; + sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 17 ; + sh:path biolink:species_context_qualifier ], + [ sh:class biolink:NamedThing ; + sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:broad_match ], [ sh:datatype xsd:string ; sh:description "A high-level grouping for the relationship type. AKA minimal predicate. This is analogous to category for nodes." ; sh:maxCount 1 ; @@ -34927,41 +34948,27 @@ biolink:PredicateMapping a sh:NodeShape ; sh:order 7 ; sh:path rdf:predicate ], [ sh:datatype xsd:string ; - sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:mapped_predicate ], - [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:object_derivative_qualifier ], - [ sh:class biolink:OrganismTaxon ; - sh:description "A statement qualifier representing a taxonomic category of species in which a relationship expressed in an association took place." ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 17 ; - sh:path biolink:species_context_qualifier ], + sh:order 6 ; + sh:path biolink:subject_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; + sh:description "The predicate that is being replaced by the fully qualified representation of predicate + subject and object qualifiers. Only to be used in test data and mapping data to help with the transition to the fully qualified predicate model. Not to be used in knowledge graphs." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:anatomical_context_qualifier ], + sh:order 0 ; + sh:path biolink:mapped_predicate ], [ sh:datatype xsd:string ; - sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:subject_part_qualifier ], + sh:order 14 ; + sh:path biolink:object_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:subject_derivative_qualifier ], + sh:order 3 ; + sh:path biolink:subject_form_or_variant_qualifier ], [ sh:datatype xsd:string ; sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the subject of an association (aka: statement)." ; sh:maxCount 1 ; @@ -34969,138 +34976,131 @@ biolink:PredicateMapping a sh:NodeShape ; sh:order 1 ; sh:path biolink:subject_aspect_qualifier ], [ sh:datatype xsd:string ; - sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:description "A statement qualifier representing an anatomical location where an relationship expressed in an association took place (can be a tissue, cell type, or sub-cellular location)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:object_part_qualifier ], + sh:order 16 ; + sh:path biolink:anatomical_context_qualifier ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:object_form_or_variant_qualifier ], - [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the object of an association (aka: statement)." ; - sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; + sh:order 9 ; + sh:path biolink:object_aspect_qualifier ], + [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the object of an association (or statement)." ; sh:maxCount 1 ; - sh:order 10 ; - sh:path biolink:object_direction_qualifier ], + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:object_derivative_qualifier ], [ sh:datatype xsd:string ; - sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the subject of an association (aka: statement)." ; + sh:description "A qualifier that composes with a core subject/object concept to describe something that is derived from the core concept. For example, the qualifier ‘metabolite’ combines with a ‘Chemical X’ core concept to express the composed concept ‘a metabolite of Chemical X’. This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:subject_form_or_variant_qualifier ], + sh:order 5 ; + sh:path biolink:subject_derivative_qualifier ], [ sh:datatype xsd:string ; + sh:description "A qualifier that composes with a core subject/object concept to define a specific type, variant, alternative version of this concept. The composed concept remains a subtype or instance of the core concept. For example, the qualifier ‘mutation’ combines with the core concept ‘Gene X’ to express the compose concept ‘a mutation of Gene X’. This qualifier specifies a change in the object of an association (aka: statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:object_context_qualifier ], + sh:order 11 ; + sh:path biolink:object_form_or_variant_qualifier ], [ sh:description "Composes with the core concept (+ aspect if provided) to describe a change in its direction or degree. This qualifier qualifies the subject of an association (aka: statement)." ; sh:in ( "increased" "upregulated" "decreased" "downregulated" ) ; sh:maxCount 1 ; sh:order 2 ; sh:path biolink:subject_direction_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "a list of terms from different schemas or terminology systems that have a broader, more general meaning. Broader terms are typically shown as parents in a hierarchy or tree." ; - sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:broad_match ], [ sh:datatype xsd:string ; - sh:description "Composes with the core concept to describe new concepts of a different ontological type. e.g. a process in which the core concept participates, a function/activity/role held by the core concept, or a characteristic/quality that inheres in the core concept. The purpose of the aspect slot is to indicate what aspect is being affected in an 'affects' association. This qualifier specifies a change in the object of an association (aka: statement)." ; + sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the subject of an association (or statement)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:object_aspect_qualifier ], - [ sh:class biolink:NamedThing ; - sh:description "holds between two entities that have strictly equivalent meanings, with a high degree of confidence" ; - sh:nodeKind sh:IRI ; - sh:order 18 ; - sh:path biolink:exact_match ], + sh:order 4 ; + sh:path biolink:subject_part_qualifier ], + [ sh:datatype xsd:string ; + sh:description "defines a specific part/component of the core concept (used in cases there this specific part has no IRI we can use to directly represent it, e.g. 'ESR1 transcript' q: polyA tail). This qualifier is for the object of an association (or statement)." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:object_part_qualifier ], [ sh:datatype xsd:string ; sh:description "Predicate to be used in an association when subject and object qualifiers are present and the full reading of the statement requires a qualification to the predicate in use in order to refine or increase the specificity of the full statement reading. This qualifier holds a relationship to be used instead of that expressed by the primary predicate, in a ‘full statement’ reading of the association, where qualifier-based semantics are included. This is necessary only in cases where the primary predicate does not work in a full statement reading." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; - sh:path biolink:qualified_predicate ], - [ sh:description "A statement qualifier representing a type of molecular control mechanism through which an effect of a chemical on a gene or gene product is mediated (e.g. 'agonism', 'inhibition', 'allosteric modulation', 'channel blocker')" ; - sh:in ( "binding" "inhibition" "antibody_inhibition" "antagonism" "molecular_channel_blockage" "inverse_agonism" "negative_allosteric_modulation" "agonism" "molecular_channel_opening" "positive_allosteric_modulation" "potentiation" "activation" "inducer" "transcriptional_regulation" "signaling_mediated_control" "stabilization" "stimulation" "releasing_activity" ) ; - sh:maxCount 1 ; - sh:order 15 ; - sh:path biolink:causal_mechanism_qualifier ] ; + sh:path biolink:qualified_predicate ] ; sh:targetClass biolink:PredicateMapping . biolink:Procedure a sh:NodeShape ; sh:closed true ; sh:description "A series of actions conducted in a certain order or manner" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 10 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ], + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ] ; + sh:order 2 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Procedure . biolink:SocioeconomicAttribute a sh:NodeShape ; @@ -35112,50 +35112,33 @@ biolink:SocioeconomicAttribute a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], [ sh:class biolink:QuantityValue ; sh:description "connects an attribute to a value" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:order 4 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -35167,18 +35150,17 @@ biolink:SocioeconomicAttribute a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -35186,12 +35168,30 @@ biolink:SocioeconomicAttribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ] ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ] ; sh:targetClass biolink:SocioeconomicAttribute . biolink:TaxonomicRank a sh:NodeShape ; @@ -35211,39 +35211,33 @@ biolink:Treatment a sh:NodeShape ; sh:closed true ; sh:description "A treatment is targeted at a disease or phenotype and may involve multiple drug 'exposures', medical devices and/or procedures" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 5 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:provided_by ], - [ sh:class biolink:Drug ; - sh:description "connects an entity to one or more drugs" ; + [ sh:class biolink:Device ; + sh:description "connects an entity to one or more (medical) devices" ; sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_drug ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:has_device ], [ sh:class biolink:Procedure ; sh:description "connects an entity to one or more (medical) procedures" ; sh:nodeKind sh:IRI ; @@ -35255,109 +35249,113 @@ biolink:Treatment a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:class biolink:Device ; - sh:description "connects an entity to one or more (medical) devices" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_device ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path dct:description ], + [ sh:class biolink:Drug ; + sh:description "connects an entity to one or more drugs" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_drug ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:time ; sh:description "a point in time" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:timepoint ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ] ; + sh:order 6 ; + sh:path biolink:full_name ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Treatment . biolink:Zygosity a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:property [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; sh:maxCount 1 ; @@ -35370,25 +35368,27 @@ biolink:Zygosity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:iri ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; - sh:maxCount 1 ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ] ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path biolink:deprecated ] ; sh:targetClass biolink:Zygosity . biolink:Case a sh:NodeShape ; @@ -35396,24 +35396,21 @@ biolink:Case a sh:NodeShape ; sh:description "An individual (human) organism that has a patient role in some clinical context." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -35421,69 +35418,88 @@ biolink:Case a sh:NodeShape ; sh:order 13 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ] ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Case . biolink:CellLine a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -35492,27 +35508,15 @@ biolink:CellLine a sh:NodeShape ; sh:order 6 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -35520,42 +35524,38 @@ biolink:CellLine a sh:NodeShape ; sh:order 11 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:class biolink:Attribute ; sh:description "may often be an organism attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ] ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:CellLine . biolink:IndividualOrganism a sh:NodeShape ; @@ -35563,59 +35563,41 @@ biolink:IndividualOrganism a sh:NodeShape ; sh:description "An instance of an organism. For example, Richard Nixon, Charles Darwin, my pet cat. Example ID: ORCID:0000-0002-5355-2576" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -35623,11 +35605,12 @@ biolink:IndividualOrganism a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -35639,7 +35622,24 @@ biolink:IndividualOrganism a sh:NodeShape ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:iri ] ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ] ; sh:targetClass biolink:IndividualOrganism . biolink:Outcome a sh:NodeShape ; @@ -35652,41 +35652,44 @@ biolink:Transcript a sh:NodeShape ; sh:closed true ; sh:description "An RNA synthesized on a DNA or RNA template by an RNA polymerase." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -35699,108 +35702,62 @@ biolink:Transcript a sh:NodeShape ; sh:order 12 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ] ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:Transcript . biolink:BiologicalProcess a sh:NodeShape ; sh:closed true ; sh:description "One or more causally connected executions of molecular functions" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -35814,21 +35771,64 @@ biolink:BiologicalProcess a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:in_taxon_label ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], + sh:order 3 ; + sh:path biolink:enabled_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], [ sh:class biolink:NamedThing ; sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; sh:nodeKind sh:IRI ; sh:order 2 ; sh:path biolink:has_output ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; - sh:path biolink:has_attribute ] ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ] ; sh:targetClass biolink:BiologicalProcess . biolink:Drug a sh:NodeShape ; @@ -35836,41 +35836,50 @@ biolink:Drug a sh:NodeShape ; sh:description "A substance intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], + sh:order 18 ; + sh:path dct:description ], + [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:highest_FDA_approval_status ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path biolink:full_name ], [ sh:description "the method or process of administering a pharmaceutical compound to achieve a therapeutic effect in humans or animals." ; sh:in ( "inhalation" "oral" "absorption_through_the_skin" "intravenous_injection" ) ; sh:order 4 ; sh:path biolink:routes_of_delivery ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; + sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; + sh:maxCount 1 ; + sh:order 3 ; + sh:path biolink:drug_regulatory_status_world_wide ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:xref ], + sh:order 14 ; + sh:path biolink:iri ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 19 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:provided_by ], + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -35879,15 +35888,16 @@ biolink:Drug a sh:NodeShape ; sh:order 0 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:boolean ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], + sh:order 8 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; @@ -35895,15 +35905,16 @@ biolink:Drug a sh:NodeShape ; sh:order 5 ; sh:path biolink:trade_name ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], + sh:order 7 ; + sh:path biolink:max_tolerated_dose ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_chemical_role ], [ sh:datatype xsd:string ; sh:description "" ; sh:maxCount 1 ; @@ -35916,39 +35927,28 @@ biolink:Drug a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 20 ; sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:category ], - [ sh:description "An agglomeration of drug regulatory status worldwide. Not specific to FDA." ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 3 ; - sh:path biolink:drug_regulatory_status_world_wide ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:max_tolerated_dose ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; + sh:order 17 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], - [ sh:description "Should be the highest level of FDA approval this chemical entity or device has, regardless of which disease, condition or phenotype it is currently being reviewed to treat. For specific levels of FDA approval for a specific condition, disease, phenotype, etc., see the association slot, 'clinical approval status.'" ; - sh:in ( "discovery_and_development_phase" "preclinical_research_phase" "fda_clinical_research_phase" "fda_review_phase_4" "fda_post_market_safety_review" "fda_clinical_research_phase_1" "fda_clinical_research_phase_2" "fda_clinical_research_phase_3" "fda_clinical_research_phase_4" "fda_fast_track" "fda_breakthrough_therapy" "fda_accelerated_approval" "fda_priority_review" "regular_fda_approval" "post_approval_withdrawal" ) ; - sh:maxCount 1 ; - sh:order 2 ; - sh:path biolink:highest_FDA_approval_status ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_chemical_role ] ; + sh:order 11 ; + sh:path biolink:xref ] ; sh:targetClass biolink:Drug . biolink:ExposureEvent a sh:NodeShape ; @@ -35974,43 +35974,29 @@ biolink:MaterialSample a sh:NodeShape ; sh:closed true ; sh:description "A sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. [SIO]" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], + sh:order 8 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -36018,11 +36004,6 @@ biolink:MaterialSample a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:id ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -36030,40 +36011,62 @@ biolink:MaterialSample a sh:NodeShape ; sh:order 9 ; sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ] ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:MaterialSample . biolink:Pathway a sh:NodeShape ; sh:closed true ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:category ], + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_input ], + [ sh:class biolink:NamedThing ; + sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -36076,104 +36079,73 @@ biolink:Pathway a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:class biolink:PhysicalEntity ; - sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:enabled_by ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an input into the process" ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_input ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 0 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:class biolink:PhysicalEntity ; + sh:description "holds between a process and a physical entity, where the physical entity executes the process" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:enabled_by ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], - [ sh:class biolink:NamedThing ; - sh:description "holds between a process and a continuant, where the continuant is an output of the process" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ] ; + sh:path biolink:in_taxon_label ] ; sh:targetClass biolink:Pathway . biolink:LifeStage a sh:NodeShape ; sh:closed true ; sh:description "A stage of development or growth of an organism, including post-natal adult stages" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; @@ -36185,23 +36157,18 @@ biolink:LifeStage a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -36213,16 +36180,49 @@ biolink:LifeStage a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 0 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ] ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:LifeStage . biolink:NucleicAcidEntity a sh:NodeShape ; @@ -36230,11 +36230,27 @@ biolink:NucleicAcidEntity a sh:NodeShape ; sh:description "A nucleic acid entity is a molecular entity characterized by availability in gene databases of nucleotide-based sequence representations of its precise sequence; for convenience of representation, partial sequences of various kinds are included." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + sh:description "" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:in_taxon_label ], + sh:order 5 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:provided_by ], + [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; + sh:nodeKind sh:IRI ; + sh:order 9 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "connects a genomic feature to its sequence" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; @@ -36247,204 +36263,188 @@ biolink:NucleicAcidEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:is_metabolite ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 19 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path rdfs:label ], + sh:order 20 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:has_biological_sequence ], + sh:order 12 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 15 ; + sh:path biolink:category ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 6 ; + sh:path biolink:available_from ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:max_tolerated_dose ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 9 ; - sh:path biolink:has_chemical_role ], + sh:order 14 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:trade_name ], + sh:order 3 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:full_name ], + sh:order 2 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 18 ; sh:path dct:description ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 6 ; - sh:path biolink:available_from ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:in_taxon ], + sh:order 19 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:iri ], + sh:order 16 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:provided_by ], + sh:order 7 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 20 ; - sh:path biolink:deprecated ], + sh:order 17 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:id ] ; + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:NucleicAcidEntity . biolink:MolecularActivity a sh:NodeShape ; sh:closed true ; sh:description "An execution of a molecular function carried out by a gene product or macromolecular complex." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path dct:description ], + sh:property [ sh:class biolink:MolecularEntity ; + sh:description "A chemical entity that is the output for the reaction" ; + sh:nodeKind sh:IRI ; + sh:order 2 ; + sh:path biolink:has_output ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:id ], [ sh:class biolink:MacromolecularMachineMixin ; sh:description "The gene product, gene, or complex that catalyzes the reaction" ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 3 ; sh:path biolink:enabled_by ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; - sh:order 15 ; - sh:path biolink:has_attribute ], + sh:order 4 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path rdfs:label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:full_name ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], + sh:order 12 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 15 ; + sh:path biolink:has_attribute ], [ sh:class biolink:MolecularEntity ; sh:description "A chemical entity that is the input for the reaction" ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_input ], - [ sh:class biolink:MolecularEntity ; - sh:description "A chemical entity that is the output for the reaction" ; - sh:nodeKind sh:IRI ; - sh:order 2 ; - sh:path biolink:has_output ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:MolecularActivity . biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; @@ -36452,6 +36452,38 @@ biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:description "A collection of individuals from the same taxonomic class distinguished by one or more characteristics. Characteristics can include, but are not limited to, shared geographic location, genetics, phenotypes." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; @@ -36469,72 +36501,40 @@ biolink:PopulationOfIndividualOrganisms a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ] ; + sh:order 8 ; + sh:path biolink:category ] ; sh:targetClass biolink:PopulationOfIndividualOrganisms . biolink:MacromolecularMachineMixin a sh:NodeShape ; sh:closed false ; sh:description "A union of gene locus, gene product, and macromolecular complex. These are the basic units of function in a cell. They either carry out individual biological activities, or they encode molecules which do this." ; - sh:ignoredProperties ( biolink:xref rdf:type biolink:synonym ) ; + sh:ignoredProperties ( biolink:xref biolink:synonym rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; @@ -36546,17 +36546,46 @@ biolink:MacromolecularMachineMixin a sh:NodeShape ; biolink:MolecularEntity a sh:NodeShape ; sh:closed true ; sh:description "A molecular entity is a chemical entity composed of individual or covalently bonded atoms." ; - sh:ignoredProperties ( biolink:in_taxon rdf:type biolink:in_taxon_label biolink:has_biological_sequence ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:ignoredProperties ( biolink:has_biological_sequence rdf:type biolink:in_taxon_label biolink:in_taxon ) ; + sh:property [ sh:class biolink:ChemicalRole ; + sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; - sh:order 16 ; - sh:path biolink:has_attribute ], + sh:order 5 ; + sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:trade_name ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:is_toxic ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -36569,12 +36598,17 @@ biolink:MolecularEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "indicates whether a molecular entity is a metabolite" ; + [ sh:datatype xsd:string ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:is_metabolite ], + sh:order 3 ; + sh:path biolink:max_tolerated_dose ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 13 ; @@ -36585,68 +36619,34 @@ biolink:MolecularEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path rdfs:label ], - [ sh:class biolink:ChemicalRole ; - sh:description "A role is particular behaviour which a chemical entity may exhibit." ; - sh:nodeKind sh:IRI ; - sh:order 5 ; - sh:path biolink:has_chemical_role ], - [ sh:datatype xsd:string ; - sh:description "" ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:trade_name ], - [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; + sh:order 17 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:boolean ; + sh:description "indicates whether a molecular entity is a metabolite" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:max_tolerated_dose ], + sh:order 0 ; + sh:path biolink:is_metabolite ], [ sh:description "" ; sh:in ( "over_the_counter" "prescription" ) ; sh:order 2 ; sh:path biolink:available_from ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 16 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:iri ], - [ sh:datatype xsd:boolean ; - sh:description "" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:is_toxic ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 17 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ] ; + sh:path biolink:id ] ; sh:targetClass biolink:MolecularEntity . biolink:PhysicalEntity a sh:NodeShape ; @@ -36659,44 +36659,34 @@ biolink:PhysicalEntity a sh:NodeShape ; sh:order 3 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; + sh:order 4 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 1 ; + sh:path biolink:xref ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -36709,17 +36699,27 @@ biolink:PhysicalEntity a sh:NodeShape ; sh:order 0 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:full_name ], + sh:order 5 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:category ] ; + sh:path biolink:category ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ] ; sh:targetClass biolink:PhysicalEntity . biolink:ChemicalEntityOrGeneOrGeneProduct a sh:NodeShape ; @@ -36738,22 +36738,11 @@ biolink:Genotype a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:class biolink:Zygosity ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_zygosity ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; @@ -36766,61 +36755,72 @@ biolink:Genotype a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:in_taxon ], + sh:order 2 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + [ sh:class biolink:Zygosity ; sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_zygosity ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:order 10 ; + sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:id ] ; + sh:path rdfs:label ] ; sh:targetClass biolink:Genotype . biolink:SequenceVariant a sh:NodeShape ; @@ -36828,50 +36828,63 @@ biolink:SequenceVariant a sh:NodeShape ; sh:description "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 12 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:id ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], + sh:order 9 ; + sh:path biolink:iri ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:in_taxon_label ], + sh:order 15 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 2 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], + sh:order 7 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; @@ -36883,116 +36896,105 @@ biolink:SequenceVariant a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:has_biological_sequence ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], [ sh:class biolink:OrganismTaxon ; sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; sh:nodeKind sh:IRI ; sh:order 3 ; sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:xref ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], [ sh:class biolink:Gene ; sh:description "Each allele can be associated with any number of genes" ; sh:nodeKind sh:IRI ; sh:order 0 ; - sh:path biolink:has_gene ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ] ; + sh:path biolink:has_gene ] ; sh:targetClass biolink:SequenceVariant . biolink:ChemicalEntity a sh:NodeShape ; sh:closed true ; sh:description "A chemical entity is a physical entity that pertains to chemistry or biochemistry." ; - sh:ignoredProperties ( biolink:in_taxon biolink:drug_regulatory_status_world_wide biolink:is_supplement biolink:routes_of_delivery biolink:highest_FDA_approval_status biolink:is_metabolite rdf:type biolink:in_taxon_label biolink:has_biological_sequence ) ; + sh:ignoredProperties ( biolink:in_taxon rdf:type biolink:is_metabolite biolink:routes_of_delivery biolink:is_supplement biolink:has_biological_sequence biolink:highest_FDA_approval_status biolink:in_taxon_label biolink:drug_regulatory_status_world_wide ) ; sh:property [ sh:datatype xsd:string ; + sh:description "" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path biolink:trade_name ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:synonym ], + sh:order 5 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:provided_by ], [ sh:class biolink:ChemicalRole ; sh:description "A role is particular behaviour which a chemical entity may exhibit." ; sh:nodeKind sh:IRI ; sh:order 4 ; sh:path biolink:has_chemical_role ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:id ], + [ sh:description "" ; + sh:in ( "over_the_counter" "prescription" ) ; + sh:order 1 ; + sh:path biolink:available_from ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path biolink:category ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path rdfs:label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:id ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 15 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "" ; + sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:trade_name ], - [ sh:description "" ; - sh:in ( "over_the_counter" "prescription" ) ; - sh:order 1 ; - sh:path biolink:available_from ], + sh:order 2 ; + sh:path biolink:max_tolerated_dose ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:full_name ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 16 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:boolean ; sh:description "" ; sh:maxCount 1 ; @@ -37005,72 +37007,72 @@ biolink:ChemicalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:xref ], + sh:order 8 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "The highest dose of a drug or treatment that does not cause unacceptable side effects. The maximum tolerated dose is determined in clinical trials by testing increasing doses on different groups of people until the highest dose with acceptable side effects is found. Also called MTD." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:max_tolerated_dose ] ; + sh:order 12 ; + sh:path rdf:type ] ; sh:targetClass biolink:ChemicalEntity . biolink:Agent a sh:NodeShape ; sh:closed true ; sh:description "person, group, organization or project that provides a piece of information (i.e. a knowledge association)" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 4 ; sh:path biolink:full_name ], + [ sh:datatype xsd:anyURI ; + sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:affiliation ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 1 ; + sh:path biolink:address ], [ sh:datatype xsd:string ; - sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "a professional relationship between one provider (often a person) within another provider (often an organization). Target provider identity should be specified by a CURIE. Providers may have multiple affiliations." ; + sh:order 11 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "it is recommended that an author's 'name' property be formatted as \"surname, firstname initial.\"" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:affiliation ], + sh:order 10 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "Different classes of agents have distinct preferred identifiers. For publishers, use the ISBN publisher code. See https://grp.isbn-international.org/ for publisher code lookups. For editors, authors and individual providers, use the individual's ORCID if available; Otherwise, a ScopusID, ResearchID or Google Scholar ID ('GSID') may be used if the author ORCID is unknown. Institutional agents could be identified by an International Standard Name Identifier ('ISNI') code." ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -37078,57 +37080,55 @@ biolink:Agent a sh:NodeShape ; sh:order 8 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "the particulars of the place where someone or an organization is situated. For now, this slot is a simple text \"blob\" containing all relevant details of the given location for fitness of purpose. For the moment, this \"address\" can include other contact details such as email and phone number(?)." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:address ] ; + sh:order 7 ; + sh:path biolink:iri ] ; sh:targetClass biolink:Agent . biolink:PhenotypicFeature a sh:NodeShape ; sh:closed true ; sh:description "A combination of entity and quality that makes up a phenotyping statement. An observable characteristic of an individual resulting from the interaction of its genotype with its molecular and physical environment." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:property [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -37136,65 +37136,65 @@ biolink:PhenotypicFeature a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:id ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ] ; + sh:path biolink:iri ] ; sh:targetClass biolink:PhenotypicFeature . biolink:ChemicalRole a sh:NodeShape ; sh:closed true ; sh:description "A role played by the molecular entity or part thereof within a chemical context." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:property [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 9 ; + sh:path biolink:synonym ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -37203,27 +37203,14 @@ biolink:ChemicalRole a sh:NodeShape ; sh:order 1 ; sh:path biolink:has_attribute_type ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], + sh:order 13 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -37236,22 +37223,12 @@ biolink:ChemicalRole a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], + sh:order 12 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -37259,6 +37236,28 @@ biolink:ChemicalRole a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; @@ -37266,186 +37265,174 @@ biolink:ChemicalRole a sh:NodeShape ; sh:order 14 ; sh:path biolink:deprecated ], [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], + sh:order 0 ; + sh:path rdfs:label ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ] ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:ChemicalRole . biolink:DiseaseOrPhenotypicFeature a sh:NodeShape ; sh:closed true ; sh:description "Either one of a disease or an individual phenotypic feature. Some knowledge resources such as Monarch treat these as distinct, others such as MESH conflate. Please see definitions of phenotypic feature and disease in this model for their independent descriptions. This class is helpful to enforce domains and ranges that may involve either a disease or a phenotypic feature." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:string ; + sh:property [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 12 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ] ; - sh:targetClass biolink:DiseaseOrPhenotypicFeature . - -biolink:Gene a sh:NodeShape ; - sh:closed true ; - sh:description "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 4 ; - sh:path biolink:in_taxon ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:id ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; + sh:order 1 ; sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "connects a genomic feature to its sequence" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:has_biological_sequence ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ] ; + sh:targetClass biolink:DiseaseOrPhenotypicFeature . + +biolink:Gene a sh:NodeShape ; + sh:closed true ; + sh:description "A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene locus may include regulatory regions, transcribed regions and/or other functional sequence regions." ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], + sh:order 5 ; + sh:path biolink:in_taxon_label ], [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 12 ; sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path dct:description ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 14 ; sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:synonym ], [ sh:datatype xsd:string ; - sh:description "Symbol for a particular thing" ; + sh:description "connects a genomic feature to its sequence" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:symbol ], + sh:order 2 ; + sh:path biolink:has_biological_sequence ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path dct:description ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:order 15 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:description "Symbol for a particular thing" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], + sh:order 0 ; + sh:path biolink:symbol ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 4 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 11 ; @@ -37454,7 +37441,20 @@ biolink:Gene a sh:NodeShape ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:xref ] ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:id ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:full_name ] ; sh:targetClass biolink:Gene . biolink:BiologicalSex a sh:NodeShape ; @@ -37465,24 +37465,13 @@ biolink:BiologicalSex a sh:NodeShape ; sh:nodeKind sh:BlankNodeOrIRI ; sh:order 2 ; sh:path biolink:has_quantitative_value ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:class biolink:OntologyClass ; - sh:description "connects an attribute to a class that describes it" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 1 ; - sh:path biolink:has_attribute_type ], + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; @@ -37499,46 +37488,57 @@ biolink:BiologicalSex a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:class biolink:OntologyClass ; + sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 1 ; + sh:path biolink:has_attribute_type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 0 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:id ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 14 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], [ sh:class biolink:NamedThing ; sh:description "connects an attribute to a value" ; sh:maxCount 1 ; @@ -37552,15 +37552,34 @@ biolink:AnatomicalEntity a sh:NodeShape ; sh:description "A subcellular location, cell type or gross anatomical part" ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:iri ], + [ sh:class biolink:Attribute ; + sh:description "may often be an organism attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:provided_by ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 6 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -37573,68 +37592,49 @@ biolink:AnatomicalEntity a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 11 ; sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:xref ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:description "The human readable scientific name for the taxon of the entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 1 ; sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:id ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "may often be an organism attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], [ sh:datatype xsd:boolean ; sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path biolink:deprecated ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdf:type ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path rdfs:label ] ; + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ] ; sh:targetClass biolink:AnatomicalEntity . biolink:GeneOrGeneProduct a sh:NodeShape ; sh:closed false ; sh:description "A union of gene loci or gene products. Frequently an identifier for one will be used as proxy for another" ; - sh:ignoredProperties ( biolink:xref rdf:type biolink:synonym ) ; + sh:ignoredProperties ( biolink:xref biolink:synonym rdf:type ) ; sh:property [ sh:datatype xsd:string ; sh:description "genes are typically designated by a short symbol and a full name. We map the symbol to the default display name and use an additional slot for full name" ; sh:maxCount 1 ; @@ -37647,18 +37647,18 @@ biolink:QuantityValue a sh:NodeShape ; sh:closed true ; sh:description "A value of an attribute that is quantitative and measurable, expressed as a combination of a unit and a numeric value" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:double ; - sh:description "connects a quantity value to a number" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:has_numeric_value ], - [ sh:datatype ; + sh:property [ sh:datatype ; sh:description "connects a quantity value to a unit" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 0 ; - sh:path biolink:has_unit ] ; + sh:path biolink:has_unit ], + [ sh:datatype xsd:double ; + sh:description "connects a quantity value to a number" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:has_numeric_value ] ; sh:targetClass biolink:QuantityValue . biolink:Disease a sh:NodeShape ; @@ -37666,101 +37666,115 @@ biolink:Disease a sh:NodeShape ; sh:description "A disorder of structure or function, especially one that produces specific signs, phenotypes or symptoms or that affects a specific location and is not simply a direct result of physical injury. A disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:description "The human readable scientific name for the taxon of the entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:provided_by ], + sh:order 1 ; + sh:path biolink:in_taxon_label ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path rdfs:label ], - [ sh:class biolink:OrganismTaxon ; - sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:in_taxon ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 12 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:synonym ], + sh:order 3 ; + sh:path biolink:xref ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 13 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:full_name ], + sh:order 7 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:category ], + [ sh:class biolink:OrganismTaxon ; + sh:description "connects an entity to its taxonomic classification. Only certain kinds of entities can be taxonomically classified; see 'thing with taxon'" ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:in_taxon ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path rdf:type ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "The human readable scientific name for the taxon of the entity." ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:in_taxon_label ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; + sh:order 2 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:deprecated ], + sh:order 5 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; - sh:path biolink:id ] ; + sh:path biolink:id ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 12 ; + sh:path biolink:has_attribute ] ; sh:targetClass biolink:Disease . biolink:OrganismTaxon a sh:NodeShape ; sh:closed true ; sh:description "A classification of a set of organisms. Example instances: NCBITaxon:9606 (Homo sapiens), NCBITaxon:2 (Bacteria). Can also be used to represent strains or subspecies." ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:property [ sh:class biolink:TaxonomicRank ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 0 ; + sh:path biolink:has_taxonomic_rank ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:deprecated ], + sh:order 3 ; + sh:path biolink:full_name ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path rdfs:label ], + sh:order 10 ; + sh:path dct:description ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -37768,6 +37782,12 @@ biolink:OrganismTaxon a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -37775,70 +37795,44 @@ biolink:OrganismTaxon a sh:NodeShape ; sh:order 6 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path dct:description ], - [ sh:class biolink:TaxonomicRank ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:has_taxonomic_rank ], + sh:order 4 ; + sh:path biolink:synonym ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 11 ; sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:xref ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdf:type ], + sh:order 12 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:description "A human-readable name for an attribute or entity." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:synonym ], + sh:order 9 ; + sh:path rdfs:label ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:category ] ; + sh:order 2 ; + sh:path biolink:xref ] ; sh:targetClass biolink:OrganismTaxon . biolink:NamedThing a sh:NodeShape ; sh:closed true ; sh:description "a databased entity or concept/class" ; - sh:ignoredProperties ( biolink:upstream_resource_ids biolink:has_qualitative_value biolink:is_metabolite biolink:has_gene biolink:latitude biolink:enabled_by dct:distribution biolink:is_supplement biolink:symbol biolink:source_web_page biolink:has_drug biolink:longitude biolink:mesh_terms biolink:resource_id biolink:has_zygosity biolink:has_attribute_type biolink:routes_of_delivery biolink:has_chemical_role biolink:published_in schema1:logo biolink:has_biological_sequence biolink:has_taxonomic_rank biolink:has_procedure biolink:keywords biolink:has_device biolink:has_gene_or_gene_product biolink:ingest_date biolink:has_quantitative_value biolink:iso_abbreviation biolink:has_dataset biolink:has_output biolink:chapter biolink:issue dct:type biolink:summary biolink:timepoint biolink:drug_regulatory_status_world_wide biolink:license biolink:is_toxic biolink:format biolink:creation_date biolink:max_tolerated_dose biolink:resource_role biolink:distribution_download_url biolink:in_taxon_label biolink:authors biolink:available_from biolink:trade_name biolink:highest_FDA_approval_status biolink:affiliation biolink:in_taxon biolink:volume biolink:rights rdf:type biolink:address biolink:pages biolink:has_input ) ; - sh:property [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:ignoredProperties ( biolink:has_quantitative_value biolink:chapter biolink:latitude biolink:has_input biolink:summary biolink:has_gene_or_gene_product biolink:source_web_page biolink:ingest_date dct:distribution biolink:enabled_by biolink:has_procedure biolink:routes_of_delivery biolink:volume biolink:issue biolink:has_dataset dct:type biolink:resource_id biolink:has_zygosity biolink:has_gene biolink:has_qualitative_value biolink:pages biolink:has_device schema1:logo biolink:affiliation biolink:has_output biolink:in_taxon_label biolink:timepoint biolink:has_chemical_role biolink:highest_FDA_approval_status biolink:resource_role biolink:max_tolerated_dose biolink:longitude biolink:authors biolink:has_attribute_type biolink:is_toxic biolink:drug_regulatory_status_world_wide biolink:has_drug biolink:has_biological_sequence biolink:iso_abbreviation biolink:address biolink:format biolink:in_taxon rdf:type biolink:upstream_resource_ids biolink:rights biolink:trade_name biolink:mesh_terms biolink:creation_date biolink:license biolink:is_metabolite biolink:is_supplement biolink:available_from biolink:published_in biolink:symbol biolink:distribution_download_url biolink:has_taxonomic_rank biolink:keywords ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; - sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:id ], + sh:order 9 ; + sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; @@ -37846,111 +37840,137 @@ biolink:NamedThing a sh:NodeShape ; sh:order 5 ; sh:path biolink:iri ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path dct:description ], + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 0 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 2 ; + sh:path biolink:full_name ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 6 ; sh:path biolink:category ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:anyURI ; sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; sh:order 1 ; - sh:path biolink:xref ], + sh:path biolink:xref ] ; + sh:targetClass biolink:NamedThing . + +biolink:EvidenceType a sh:NodeShape ; + sh:closed true ; + sh:description "Class of evidence that supports an association" ; + sh:ignoredProperties ( rdf:type ) ; + sh:property [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:provided_by ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:license ], + [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:iri ], + [ sh:datatype xsd:string ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; + sh:maxCount 1 ; + sh:minCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:id ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 2 ; + sh:order 6 ; sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path rdf:type ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ] ; - sh:targetClass biolink:NamedThing . - -biolink:EvidenceType a sh:NodeShape ; - sh:closed true ; - sh:description "Class of evidence that supports an association" ; - sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:date ; + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 14 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 3 ; sh:path biolink:creation_date ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:iri ], + sh:order 11 ; + sh:path rdf:type ], [ sh:datatype xsd:string ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:license ], + sh:order 1 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 2 ; - sh:path biolink:format ], + sh:order 7 ; + sh:path biolink:synonym ], [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:category ], - [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; - sh:minCount 1 ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:id ], + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 13 ; sh:path dct:description ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:synonym ], + sh:order 10 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; @@ -37963,86 +37983,79 @@ biolink:EvidenceType a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:deprecated ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 14 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:rights ], - [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:full_name ] ; + sh:order 2 ; + sh:path biolink:format ] ; sh:targetClass biolink:EvidenceType . biolink:Publication a sh:NodeShape ; sh:closed true ; sh:description "Any ‘published’ piece of information. Publications are considered broadly to include any document or document part made available in print or on the web - which may include scientific journal issues, individual articles, and books - as well as things like pre-prints, white papers, patents, drug labels, web pages, protocol documents, and even a part of a publication if of significant knowledge scope (e.g. a figure, figure legend, or section highlighted by NLP)." ; - sh:ignoredProperties ( biolink:volume biolink:iso_abbreviation rdf:type biolink:published_in biolink:chapter biolink:issue ) ; + sh:ignoredProperties ( rdf:type biolink:volume biolink:issue biolink:iso_abbreviation biolink:chapter biolink:published_in ) ; sh:property [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:license ], + [ sh:datatype xsd:anyURI ; + sh:description "mesh terms tagging a publication" ; + sh:nodeKind sh:Literal ; + sh:order 4 ; + sh:path biolink:mesh_terms ], + [ sh:datatype xsd:string ; sh:description "executive summary of a publication" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:summary ], [ sh:datatype xsd:string ; - sh:maxCount 1 ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:rights ], + sh:order 11 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 19 ; - sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 21 ; - sh:path biolink:deprecated ], - [ sh:datatype xsd:date ; - sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:order 9 ; + sh:path biolink:format ], + [ sh:datatype xsd:string ; + sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 10 ; - sh:path biolink:creation_date ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; + sh:order 18 ; + sh:path rdfs:label ], + [ sh:class biolink:Agent ; + sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; sh:nodeKind sh:IRI ; - sh:order 20 ; - sh:path biolink:has_attribute ], + sh:order 0 ; + sh:path biolink:authors ], [ sh:datatype xsd:string ; - sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; - sh:minCount 1 ; + sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path dct:type ], + sh:order 13 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:pages ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 5 ; + sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 17 ; sh:path rdf:type ], - [ sh:datatype xsd:string ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:format ], + sh:order 21 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; @@ -38057,63 +38070,50 @@ biolink:Publication a sh:NodeShape ; sh:order 14 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "the 'title' of the publication is generally recorded in the 'name' property (inherited from NamedThing). The field name 'title' is now also tagged as an acceptable alias for the node property 'name' (just in case)." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path rdfs:label ], + sh:order 19 ; + sh:path dct:description ], [ sh:datatype xsd:string ; - sh:description "When a 2-tuple of page numbers are provided, they represent the start and end page of the publication within its parent publication context. For books, this may be set to the total number of pages of the book." ; + sh:description "Ontology term for publication type may be drawn from Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/), FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html), the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html), the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres (http://vocabularies.coar-repositories.org/documentation/resource_types/), Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or equivalent publication type ontology. When a given publication type ontology term is used within a given knowledge graph, then the CURIE identified term must be documented in the graph as a concept node of biolink:category biolink:OntologyClass." ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:pages ], + sh:order 6 ; + sh:path dct:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 20 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:date ; + sh:description "date on which an entity was created. This can be applied to nodes or edges" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 10 ; + sh:path biolink:creation_date ], + [ sh:datatype xsd:string ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 8 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 15 ; sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:provided_by ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; sh:order 16 ; sh:path biolink:category ], - [ sh:datatype xsd:anyURI ; - sh:description "mesh terms tagging a publication" ; - sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:mesh_terms ], [ sh:datatype xsd:string ; sh:description "keywords tagging a publication" ; sh:nodeKind sh:Literal ; sh:order 3 ; - sh:path biolink:keywords ], - [ sh:class biolink:Agent ; - sh:description "connects an publication to the list of authors who contributed to the publication. This property should be a comma-delimited list of author names. It is recommended that an author's name be formatted as \"surname, firstname initial.\". Note that this property is a node annotation expressing the citation list of authorship which might typically otherwise be more completely documented in biolink:PublicationToProviderAssociation defined edges which point to full details about an author and possibly, some qualifiers which clarify the specific status of a given author in the publication." ; - sh:nodeKind sh:IRI ; - sh:order 0 ; - sh:path biolink:authors ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:license ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:xref ] ; + sh:path biolink:keywords ] ; sh:targetClass biolink:Publication . biolink:RetrievalSource a sh:NodeShape ; @@ -38121,69 +38121,60 @@ biolink:RetrievalSource a sh:NodeShape ; sh:description "Provides information about how a particular InformationResource served as a source from which knowledge expressed in an Edge, or data used to generate this knowledge, was retrieved." ; sh:ignoredProperties ( rdf:type ) ; sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path biolink:iri ], + sh:order 5 ; + sh:path biolink:rights ], [ sh:datatype xsd:string ; - sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; - sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 14 ; + sh:path rdf:type ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:id ], + sh:order 13 ; + sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 16 ; - sh:path dct:description ], + sh:order 4 ; + sh:path biolink:license ], [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 18 ; - sh:path biolink:deprecated ], - [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; - sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; + sh:order 11 ; + sh:path biolink:id ], + [ sh:datatype xsd:anyURI ; + sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:maxCount 1 ; sh:minCount 1 ; - sh:order 1 ; - sh:path biolink:resource_role ], - [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; - sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 15 ; - sh:path rdfs:label ], + sh:order 0 ; + sh:path biolink:resource_id ], [ sh:datatype xsd:string ; sh:description "Alternate human-readable names for a thing" ; sh:nodeKind sh:Literal ; sh:order 10 ; sh:path biolink:synonym ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 13 ; - sh:path biolink:category ], + sh:order 18 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; sh:nodeKind sh:Literal ; sh:order 8 ; sh:path biolink:provided_by ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + [ sh:datatype xsd:string ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:xref ], + sh:order 6 ; + sh:path biolink:format ], [ sh:datatype xsd:date ; sh:description "date on which an entity was created. This can be applied to nodes or edges" ; sh:maxCount 1 ; @@ -38191,92 +38182,99 @@ biolink:RetrievalSource a sh:NodeShape ; sh:order 7 ; sh:path biolink:creation_date ], [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:license ], - [ sh:datatype xsd:anyURI ; - sh:description "The InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:order 15 ; + sh:path rdfs:label ], + [ sh:description "The role of the InformationResource in the retrieval of the knowledge expressed in an Edge, or data used to generate this knowledge." ; + sh:in ( "primary_knowledge_source" "aggregator_knowledge_source" "supporting_data_source" ) ; sh:maxCount 1 ; sh:minCount 1 ; + sh:order 1 ; + sh:path biolink:resource_role ], + [ sh:datatype xsd:string ; + sh:description "a human-readable description of an entity" ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:resource_id ], + sh:order 16 ; + sh:path dct:description ], [ sh:datatype xsd:anyURI ; sh:description "The InformationResources that served as a source for the InformationResource that served as a source for the knowledge expressed in an Edge, or data used to generate this knowledge." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:upstream_resource_ids ], - [ sh:datatype xsd:string ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:rights ], [ sh:class biolink:Attribute ; sh:description "connects any entity to an attribute" ; sh:nodeKind sh:IRI ; sh:order 17 ; sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:format ], - [ sh:datatype xsd:string ; + sh:order 12 ; + sh:path biolink:iri ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path rdf:type ] ; + sh:order 3 ; + sh:path biolink:xref ] ; sh:targetClass biolink:RetrievalSource . biolink:Study a sh:NodeShape ; sh:closed true ; sh:description "a detailed investigation and/or analysis" ; sh:ignoredProperties ( rdf:type ) ; - sh:property [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:property [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 1 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "A human-readable name for an attribute or entity." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 5 ; - sh:path biolink:iri ], + sh:order 8 ; + sh:path rdfs:label ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path biolink:provided_by ], [ sh:datatype xsd:string ; sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 2 ; sh:path biolink:full_name ], - [ sh:datatype xsd:anyURI ; - sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; - sh:minCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:category ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 10 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 1 ; - sh:path biolink:xref ], [ sh:datatype xsd:string ; sh:nodeKind sh:Literal ; sh:order 7 ; sh:path rdf:type ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 3 ; + sh:path biolink:synonym ], [ sh:datatype xsd:string ; sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; sh:order 9 ; sh:path dct:description ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path biolink:deprecated ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 10 ; + sh:path biolink:has_attribute ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -38285,69 +38283,41 @@ biolink:Study a sh:NodeShape ; sh:order 4 ; sh:path biolink:id ], [ sh:datatype xsd:string ; - sh:description "A human-readable name for an attribute or entity." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path rdfs:label ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:order 5 ; + sh:path biolink:iri ], + [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path biolink:provided_by ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; + sh:order 11 ; + sh:path biolink:deprecated ], + [ sh:datatype xsd:anyURI ; + sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; + sh:minCount 1 ; sh:nodeKind sh:Literal ; - sh:order 3 ; - sh:path biolink:synonym ] ; + sh:order 6 ; + sh:path biolink:category ] ; sh:targetClass biolink:Study . biolink:Attribute a sh:NodeShape ; sh:closed true ; sh:description "A property or characteristic of an entity. For example, an apple may have properties such as color, shape, age, crispiness. An environmental sample may have attributes such as depth, lat, long, material." ; - sh:ignoredProperties ( biolink:in_taxon biolink:timepoint biolink:has_gene_or_gene_product rdf:type biolink:in_taxon_label biolink:has_biological_sequence ) ; - sh:property [ sh:datatype xsd:string ; - sh:nodeKind sh:Literal ; - sh:order 11 ; - sh:path rdf:type ], - [ sh:class biolink:Attribute ; - sh:description "connects any entity to an attribute" ; - sh:nodeKind sh:IRI ; - sh:order 13 ; - sh:path biolink:has_attribute ], - [ sh:datatype xsd:string ; - sh:description "a long-form human readable name for a thing" ; + sh:ignoredProperties ( biolink:in_taxon rdf:type biolink:has_biological_sequence biolink:has_gene_or_gene_product biolink:in_taxon_label biolink:timepoint ) ; + sh:property [ sh:datatype xsd:boolean ; + sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 8 ; - sh:path biolink:full_name ], - [ sh:datatype xsd:string ; - sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; - sh:nodeKind sh:Literal ; - sh:order 6 ; - sh:path biolink:provided_by ], - [ sh:class biolink:QuantityValue ; - sh:description "connects an attribute to a value" ; - sh:nodeKind sh:BlankNodeOrIRI ; - sh:order 2 ; - sh:path biolink:has_quantitative_value ], - [ sh:class biolink:NamedThing ; - sh:description "connects an attribute to a value" ; - sh:maxCount 1 ; - sh:nodeKind sh:IRI ; - sh:order 3 ; - sh:path biolink:has_qualitative_value ], + sh:order 14 ; + sh:path biolink:deprecated ], [ sh:datatype xsd:string ; - sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 0 ; - sh:path rdfs:label ], - [ sh:datatype xsd:anyURI ; - sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; - sh:nodeKind sh:Literal ; - sh:order 7 ; - sh:path biolink:xref ], + sh:order 4 ; + sh:path biolink:iri ], [ sh:datatype xsd:anyURI ; sh:description "Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI. This field is multi-valued. It should include values for ancestors of the biolink class; for example, a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`. In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f` may have a rdf:type assertion to a SO class such as TF_binding_site, which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity, biolink:MolecularEntity, biolink:NamedThing}" ; sh:minCount 1 ; @@ -38355,16 +38325,17 @@ biolink:Attribute a sh:NodeShape ; sh:order 10 ; sh:path biolink:category ], [ sh:datatype xsd:string ; - sh:description "An IRI for an entity. This is determined by the id using expansion rules." ; + sh:description "a human-readable description of an entity" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 4 ; - sh:path biolink:iri ], - [ sh:datatype xsd:string ; - sh:description "Alternate human-readable names for a thing" ; - sh:nodeKind sh:Literal ; - sh:order 9 ; - sh:path biolink:synonym ], + sh:order 12 ; + sh:path dct:description ], + [ sh:class biolink:NamedThing ; + sh:description "connects an attribute to a value" ; + sh:maxCount 1 ; + sh:nodeKind sh:IRI ; + sh:order 3 ; + sh:path biolink:has_qualitative_value ], [ sh:class biolink:OntologyClass ; sh:description "connects an attribute to a class that describes it" ; sh:maxCount 1 ; @@ -38372,12 +38343,6 @@ biolink:Attribute a sh:NodeShape ; sh:nodeKind sh:IRI ; sh:order 1 ; sh:path biolink:has_attribute_type ], - [ sh:datatype xsd:string ; - sh:description "a human-readable description of an entity" ; - sh:maxCount 1 ; - sh:nodeKind sh:Literal ; - sh:order 12 ; - sh:path dct:description ], [ sh:datatype xsd:string ; sh:description "A unique identifier for an entity. Must be either a CURIE shorthand for a URI or a complete URI" ; sh:maxCount 1 ; @@ -38385,12 +38350,47 @@ biolink:Attribute a sh:NodeShape ; sh:nodeKind sh:Literal ; sh:order 5 ; sh:path biolink:id ], - [ sh:datatype xsd:boolean ; - sh:description "A boolean flag indicating that an entity is no longer considered current or valid." ; + [ sh:datatype xsd:string ; + sh:description "a long-form human readable name for a thing" ; sh:maxCount 1 ; sh:nodeKind sh:Literal ; - sh:order 14 ; - sh:path biolink:deprecated ] ; + sh:order 8 ; + sh:path biolink:full_name ], + [ sh:datatype xsd:string ; + sh:nodeKind sh:Literal ; + sh:order 11 ; + sh:path rdf:type ], + [ sh:class biolink:Attribute ; + sh:description "connects any entity to an attribute" ; + sh:nodeKind sh:IRI ; + sh:order 13 ; + sh:path biolink:has_attribute ], + [ sh:datatype xsd:anyURI ; + sh:description "A database cross reference or alternative identifier for a NamedThing or edge between two NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or gives more detail about the edge. This property can be used on a node or edge to provide multiple URIs or CURIE cross references." ; + sh:nodeKind sh:Literal ; + sh:order 7 ; + sh:path biolink:xref ], + [ sh:datatype xsd:string ; + sh:description "Alternate human-readable names for a thing" ; + sh:nodeKind sh:Literal ; + sh:order 9 ; + sh:path biolink:synonym ], + [ sh:datatype xsd:string ; + sh:description "The human-readable 'attribute name' can be set to a string which reflects its context of interpretation, e.g. SEPIO evidence/provenance/confidence annotation or it can default to the name associated with the 'has attribute type' slot ontology term." ; + sh:maxCount 1 ; + sh:nodeKind sh:Literal ; + sh:order 0 ; + sh:path rdfs:label ], + [ sh:class biolink:QuantityValue ; + sh:description "connects an attribute to a value" ; + sh:nodeKind sh:BlankNodeOrIRI ; + sh:order 2 ; + sh:path biolink:has_quantitative_value ], + [ sh:datatype xsd:string ; + sh:description "The value in this node property represents the knowledge provider that created or assembled the node and all of its attributes. Used internally to represent how a particular node made its way into a knowledge provider or graph." ; + sh:nodeKind sh:Literal ; + sh:order 6 ; + sh:path biolink:provided_by ] ; sh:targetClass biolink:Attribute . biolink:OntologyClass a sh:NodeShape ; diff --git a/src/biolink_model/datamodel/model.py b/src/biolink_model/datamodel/model.py index 3a91a8c97..85fea08d3 100644 --- a/src/biolink_model/datamodel/model.py +++ b/src/biolink_model/datamodel/model.py @@ -1,5 +1,5 @@ # Auto generated from biolink_model.yaml by pythongen.py version: 0.0.1 -# Generation date: 2025-01-09T18:18:29 +# Generation date: 2025-01-10T08:43:34 # Schema: Biolink-Model # # id: https://w3id.org/biolink/biolink-model @@ -115,7 +115,6 @@ HSAPDV = CurieNamespace('HsapDv', 'http://purl.obolibrary.org/obo/HsapDv_') IAO = CurieNamespace('IAO', 'http://purl.obolibrary.org/obo/IAO_') ICD10 = CurieNamespace('ICD10', 'https://icd.who.int/browse10/2016/en#/') -ICD11 = CurieNamespace('ICD11', 'http://id.who.int/icd/entity/') ICD9 = CurieNamespace('ICD9', 'http://translator.ncats.nih.gov/ICD9_') IDO = CurieNamespace('IDO', 'http://purl.obolibrary.org/obo/IDO_') INCHI = CurieNamespace('INCHI', 'http://identifiers.org/inchi/') diff --git a/src/biolink_model/schema/biolink_model.yaml b/src/biolink_model/schema/biolink_model.yaml index ec8d6ae48..854cc910a 100644 --- a/src/biolink_model/schema/biolink_model.yaml +++ b/src/biolink_model/schema/biolink_model.yaml @@ -8213,7 +8213,7 @@ classes: - NCIT - SNOMEDCT - medgen - - ICD11 + - icd11 - icd11.foundation - ICD10 - ICD9 diff --git a/src/biolink_model/scripts/classprefixes.py b/src/biolink_model/scripts/classprefixes.py index 34b83a3be..26a93dc9a 100644 --- a/src/biolink_model/scripts/classprefixes.py +++ b/src/biolink_model/scripts/classprefixes.py @@ -1,5 +1,5 @@ # Auto generated from class_prefixes.yaml by pythongen.py version: 0.0.1 -# Generation date: 2025-01-09T18:19:13 +# Generation date: 2025-01-10T08:44:21 # Schema: BiolinkClassPrefixes # # id: biolink-model-class-prefixes