From ec428081c94818e18c906551563b81a1503a1332 Mon Sep 17 00:00:00 2001 From: BAevermann Date: Thu, 19 Aug 2021 16:51:40 -0700 Subject: [PATCH] OGMS release ####### --- ogms.obo | 28 ++++++++++++++-------------- ogms.owl | 36 ++++++++++++++++++------------------ src/.DS_Store | Bin 8196 -> 8196 bytes src/ontology/.DS_Store | Bin 6148 -> 10244 bytes 4 files changed, 32 insertions(+), 32 deletions(-) diff --git a/ogms.obo b/ogms.obo index 467d208..410531d 100644 --- a/ogms.obo +++ b/ogms.obo @@ -1,5 +1,5 @@ format-version: 1.2 -data-version: 2021-06-28 +data-version: 2021-08-19 remark: The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.\n\nThe latest version of OGMS is available at http://purl.obolibrary.org/obo/ogms.owl\n\nThe OGMS developer site is https://github.com/OGMS/ogms\n\nIf you are interested in participating in the development of OGMS, please send email to baeverma ontology: ogms property_value: http://purl.org/dc/elements/1.1/creator "Alan Ruttenberg" xsd:string @@ -19,7 +19,7 @@ property_value: http://purl.org/dc/elements/1.1/date "2009-08-07" xsd:string property_value: http://purl.org/dc/elements/1.1/description "The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats.\n\nOGMS is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology." xsd:string property_value: http://purl.org/dc/elements/1.1/title "Ontology for General Medical Science" xsd:string property_value: http://purl.org/dc/terms/license http://creativecommons.org/licenses/by/4.0/ xsd:string -property_value: owl:versionInfo "2021-06-28" xsd:string +property_value: owl:versionInfo "2021-08-19" xsd:string owl-axioms: Prefix(owl:=)\nPrefix(rdf:=)\nPrefix(xml:=)\nPrefix(xsd:=)\nPrefix(rdfs:=)\n\n\nOntology(\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(Class())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(NamedIndividual())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\nDeclaration(AnnotationProperty())\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: (BFO OWL specification label)\n\nSubAnnotationPropertyOf( rdfs:label)\n\n# Annotation Property: (BFO CLIF specification label)\n\nSubAnnotationPropertyOf( rdfs:label)\n\n# Annotation Property: (scheduled for obsoletion on or after)\n\nAnnotationPropertyRange( xsd:dateTime)\n\n\n############################\n# Classes\n############################\n\n# Class: (entity)\n\nSubClassOf( owl:Thing)\n\n# Class: (curation status specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (obsolescence reason specification)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (denotator type)\n\nEquivalentClasses( ObjectOneOf( ))\n\n# Class: (obsolete_sign)\n\nSubClassOf( owl:Thing)\n\n\n############################\n# Named Individuals\n############################\n\n# Individual: (metadata complete)\n\n\n# Individual: (organizational term)\n\n\n# Individual: (ready for release)\n\n\n# Individual: (metadata incomplete)\n\n\n# Individual: (uncurated)\n\n\n# Individual: (pending final vetting)\n\n\n# Individual: (placeholder removed)\n\n\n# Individual: (terms merged)\n\n\n# Individual: (term imported)\n\n\n# Individual: (term split)\n\n\n# Individual: (to be replaced with external ontology term)\n\n\n# Individual: (requires discussion)\n\n\n\nDifferentIndividuals( )\nDifferentIndividuals( )\n) [Term] @@ -869,6 +869,13 @@ def: "A process that realizes a plan which is the concretization of a plan speci is_a: BFO:0000015 ! process property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl +[Term] +id: OBI:0000278 +name: disease stage +def: "a part of an occurrence of a disease process which is associated with position in the normal progression of the disease" [] +is_a: BFO:0000015 ! process +property_value: IAO:0000412 http://purl.obolibrary.org/obo/obi.owl + [Term] id: OGMS:0000014 name: clinical finding @@ -1528,7 +1535,7 @@ property_value: IAO:0000232 "creation date: 2011-09-20T09:57:44Z" xsd:string id: OGMS:0000105 name: relapse def: "A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease." [] -is_a: disease_stage ! disease stage +is_a: OBI:0000278 ! disease stage property_value: http://purl.org/dc/elements/1.1/date "10 NOV 2015" xsd:string property_value: IAO:0000116 "A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course." xsd:string property_value: IAO:0000117 "Albert Goldfain\nRichard Scheuermann\nSagar Jain" xsd:string @@ -1539,7 +1546,7 @@ property_value: IAO:0000119 http://code.google.com/p/ogms/issues/detail?id=73 xs id: OGMS:0000106 name: remission def: "A disease stage which is characterized by the lack of a manifestation of a disease" [] -is_a: disease_stage ! disease stage +is_a: OBI:0000278 ! disease stage property_value: http://purl.org/dc/elements/1.1/date "10 NOV 2015" xsd:string property_value: IAO:0000116 "A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased." xsd:string property_value: IAO:0000117 "Albert Goldfain\nRichard Scheuermann\nSagar Jain" xsd:string @@ -1623,14 +1630,14 @@ property_value: IAO:0000232 "creation date: 2018-11-27" xsd:string id: OGMS:0000117 name: asymptomatic def: "A disease stage characterized by the lack of symptoms associated with a given disease" [] -is_a: disease_stage ! disease stage +is_a: OBI:0000278 ! disease stage property_value: IAO:0000232 "creation date: 2018-11-27" xsd:string [Term] id: OGMS:0000118 name: onset def: "A disease stage that marks the beginning of a disease" [] -is_a: disease_stage ! disease stage +is_a: OBI:0000278 ! disease stage property_value: IAO:0000232 "creation date 2018-11-27" xsd:string [Term] @@ -1726,7 +1733,7 @@ is_a: OGMS:0000061 ! pathological bodily process [Term] id: OGMS:0000133 name: progression stage -is_a: disease_stage ! disease stage +is_a: OBI:0000278 ! disease stage [Term] id: OGMS:0000134 @@ -1819,10 +1826,3 @@ def: "A role borne by some material entity which can be delivered/administrated is_a: BFO:0000023 ! role property_value: IAO:0000116 "Originally OBIB_0000026" xsd:string -[Term] -id: disease_stage -name: disease stage -def: "A part of a disease course" [] -is_a: BFO:0000015 ! process -property_value: IAO:0000116 "This class should be imported from OBI. https://github.com/OGMS/ogms/issues/105" xsd:string - diff --git a/ogms.owl b/ogms.owl index e7cef51..1d66e9d 100644 --- a/ogms.owl +++ b/ogms.owl @@ -13,7 +13,7 @@ xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#" xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"> - + Alan Ruttenberg Albert Goldfain Anand Kumar @@ -40,7 +40,7 @@ The latest version of OGMS is available at http://purl.obolibrary.org/obo/ogms.o The OGMS developer site is https://github.com/OGMS/ogms If you are interested in participating in the development of OGMS, please send email to baeverma - 2021-06-28 + 2021-08-19 @@ -2593,6 +2593,17 @@ No imports + + + + + a part of an occurrence of a disease process which is associated with position in the normal progression of the disease + + disease stage + + + + @@ -3579,7 +3590,7 @@ edited date: 30 SEPT 2015 - + A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease. A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course. Albert Goldfain @@ -3596,7 +3607,7 @@ Sagar Jain - + A disease stage which is characterized by the lack of a manifestation of a disease A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased. Albert Goldfain @@ -3726,7 +3737,7 @@ Sagar Jain - + A disease stage characterized by the lack of symptoms associated with a given disease creation date: 2018-11-27 asymptomatic @@ -3737,7 +3748,7 @@ Sagar Jain - + A disease stage that marks the beginning of a disease creation date 2018-11-27 onset @@ -3894,7 +3905,7 @@ Sagar Jain - + progression stage @@ -4051,17 +4062,6 @@ Sagar Jain - - - - - A part of a disease course - This class should be imported from OBI. https://github.com/OGMS/ogms/issues/105 - disease stage - - - -