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OGMS release #######
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BAevermann committed Aug 19, 2021
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28 changes: 14 additions & 14 deletions ogms.obo
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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
Expand All @@ -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:=<http://www.w3.org/2002/07/owl#>)\nPrefix(rdf:=<http://www.w3.org/1999/02/22-rdf-syntax-ns#>)\nPrefix(xml:=<http://www.w3.org/XML/1998/namespace>)\nPrefix(xsd:=<http://www.w3.org/2001/XMLSchema#>)\nPrefix(rdfs:=<http://www.w3.org/2000/01/rdf-schema#>)\n\n\nOntology(\nDeclaration(Class(<http://purl.obolibrary.org/obo/BFO_0000001>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/IAO_0000078>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/IAO_0000225>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/IAO_0000409>))\nDeclaration(Class(<http://purl.obolibrary.org/obo/OGMS_0000024>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000002>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000103>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000120>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000121>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000122>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000123>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000124>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000125>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000226>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000227>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000228>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000229>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000410>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000420>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000421>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000423>))\nDeclaration(NamedIndividual(<http://purl.obolibrary.org/obo/IAO_0000428>))\nDeclaration(AnnotationProperty(<http://purl.obolibrary.org/obo/BFO_0000179>))\nDeclaration(AnnotationProperty(<http://purl.obolibrary.org/obo/BFO_0000180>))\nDeclaration(AnnotationProperty(<http://purl.obolibrary.org/obo/IAO_0006012>))\n############################\n# Annotation Properties\n############################\n\n# Annotation Property: <http://purl.obolibrary.org/obo/BFO_0000179> (BFO OWL specification label)\n\nSubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/BFO_0000179> rdfs:label)\n\n# Annotation Property: <http://purl.obolibrary.org/obo/BFO_0000180> (BFO CLIF specification label)\n\nSubAnnotationPropertyOf(<http://purl.obolibrary.org/obo/BFO_0000180> rdfs:label)\n\n# Annotation Property: <http://purl.obolibrary.org/obo/IAO_0006012> (scheduled for obsoletion on or after)\n\nAnnotationPropertyRange(<http://purl.obolibrary.org/obo/IAO_0006012> xsd:dateTime)\n\n\n############################\n# Classes\n############################\n\n# Class: <http://purl.obolibrary.org/obo/BFO_0000001> (entity)\n\nSubClassOf(<http://purl.obolibrary.org/obo/BFO_0000001> owl:Thing)\n\n# Class: <http://purl.obolibrary.org/obo/IAO_0000078> (curation status specification)\n\nEquivalentClasses(<http://purl.obolibrary.org/obo/IAO_0000078> ObjectOneOf(<http://purl.obolibrary.org/obo/IAO_0000002> <http://purl.obolibrary.org/obo/IAO_0000120> <http://purl.obolibrary.org/obo/IAO_0000121> <http://purl.obolibrary.org/obo/IAO_0000122> <http://purl.obolibrary.org/obo/IAO_0000123> <http://purl.obolibrary.org/obo/IAO_0000124> <http://purl.obolibrary.org/obo/IAO_0000125> <http://purl.obolibrary.org/obo/IAO_0000423> <http://purl.obolibrary.org/obo/IAO_0000428>))\n\n# Class: <http://purl.obolibrary.org/obo/IAO_0000225> (obsolescence reason specification)\n\nEquivalentClasses(<http://purl.obolibrary.org/obo/IAO_0000225> ObjectOneOf(<http://purl.obolibrary.org/obo/IAO_0000103> <http://purl.obolibrary.org/obo/IAO_0000226> <http://purl.obolibrary.org/obo/IAO_0000227> <http://purl.obolibrary.org/obo/IAO_0000228> <http://purl.obolibrary.org/obo/IAO_0000229>))\n\n# Class: <http://purl.obolibrary.org/obo/IAO_0000409> (denotator type)\n\nEquivalentClasses(<http://purl.obolibrary.org/obo/IAO_0000409> ObjectOneOf(<http://purl.obolibrary.org/obo/IAO_0000410> <http://purl.obolibrary.org/obo/IAO_0000420> <http://purl.obolibrary.org/obo/IAO_0000421>))\n\n# Class: <http://purl.obolibrary.org/obo/OGMS_0000024> (obsolete_sign)\n\nSubClassOf(<http://purl.obolibrary.org/obo/OGMS_0000024> owl:Thing)\n\n\n############################\n# Named Individuals\n############################\n\n# Individual: <http://purl.obolibrary.org/obo/IAO_0000120> (metadata complete)\n\n\n# Individual: <http://purl.obolibrary.org/obo/IAO_0000121> (organizational term)\n\n\n# Individual: <http://purl.obolibrary.org/obo/IAO_0000122> (ready for release)\n\n\n# Individual: <http://purl.obolibrary.org/obo/IAO_0000123> (metadata incomplete)\n\n\n# Individual: <http://purl.obolibrary.org/obo/IAO_0000124> (uncurated)\n\n\n# Individual: <http://purl.obolibrary.org/obo/IAO_0000125> (pending final vetting)\n\n\n# Individual: <http://purl.obolibrary.org/obo/IAO_0000226> (placeholder removed)\n\n\n# Individual: <http://purl.obolibrary.org/obo/IAO_0000227> (terms merged)\n\n\n# Individual: <http://purl.obolibrary.org/obo/IAO_0000228> (term imported)\n\n\n# Individual: <http://purl.obolibrary.org/obo/IAO_0000229> (term split)\n\n\n# Individual: <http://purl.obolibrary.org/obo/IAO_0000423> (to be replaced with external ontology term)\n\n\n# Individual: <http://purl.obolibrary.org/obo/IAO_0000428> (requires discussion)\n\n\n\nDifferentIndividuals(<http://purl.obolibrary.org/obo/IAO_0000120> <http://purl.obolibrary.org/obo/IAO_0000121> <http://purl.obolibrary.org/obo/IAO_0000122> <http://purl.obolibrary.org/obo/IAO_0000123> <http://purl.obolibrary.org/obo/IAO_0000124> <http://purl.obolibrary.org/obo/IAO_0000125> <http://purl.obolibrary.org/obo/IAO_0000423> <http://purl.obolibrary.org/obo/IAO_0000428>)\nDifferentIndividuals(<http://purl.obolibrary.org/obo/IAO_0000226> <http://purl.obolibrary.org/obo/IAO_0000227> <http://purl.obolibrary.org/obo/IAO_0000228> <http://purl.obolibrary.org/obo/IAO_0000229>)\n)

[Term]
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -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]
Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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

36 changes: 18 additions & 18 deletions ogms.owl
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Expand Up @@ -13,7 +13,7 @@
xmlns:protege="http://protege.stanford.edu/plugins/owl/protege#"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/ogms.owl">
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ogms/2021-06-28/ogms.owl"/>
<owl:versionIRI rdf:resource="http://purl.obolibrary.org/obo/ogms/2021-08-19/ogms.owl"/>
<dc:creator>Alan Ruttenberg</dc:creator>
<dc:creator>Albert Goldfain</dc:creator>
<dc:creator>Anand Kumar</dc:creator>
Expand All @@ -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</rdfs:comment>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-06-28</owl:versionInfo>
<owl:versionInfo rdf:datatype="http://www.w3.org/2001/XMLSchema#string">2021-08-19</owl:versionInfo>
</owl:Ontology>


Expand Down Expand Up @@ -2593,6 +2593,17 @@ No imports</obo:IAO_0000115>



<!-- http://purl.obolibrary.org/obo/OBI_0000278 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0000278">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000115 xml:lang="en">a part of an occurrence of a disease process which is associated with position in the normal progression of the disease</obo:IAO_0000115>
<obo:IAO_0000412 rdf:resource="http://purl.obolibrary.org/obo/obi.owl"/>
<rdfs:label xml:lang="en">disease stage</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OGMS_0000014 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000014">
Expand Down Expand Up @@ -3579,7 +3590,7 @@ edited date: 30 SEPT 2015</obo:IAO_0000232>
<!-- http://purl.obolibrary.org/obo/OGMS_0000105 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000105">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ogms.owl#disease_stage"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000278"/>
<obo:IAO_0000115>A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease.</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">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.</obo:IAO_0000116>
<obo:IAO_0000117>Albert Goldfain
Expand All @@ -3596,7 +3607,7 @@ Sagar Jain</obo:IAO_0000117>
<!-- http://purl.obolibrary.org/obo/OGMS_0000106 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000106">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ogms.owl#disease_stage"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000278"/>
<obo:IAO_0000115>A disease stage which is characterized by the lack of a manifestation of a disease</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased.</obo:IAO_0000116>
<obo:IAO_0000117>Albert Goldfain
Expand Down Expand Up @@ -3726,7 +3737,7 @@ Sagar Jain</obo:IAO_0000117>
<!-- http://purl.obolibrary.org/obo/OGMS_0000117 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000117">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ogms.owl#disease_stage"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000278"/>
<obo:IAO_0000115>A disease stage characterized by the lack of symptoms associated with a given disease</obo:IAO_0000115>
<obo:IAO_0000232>creation date: 2018-11-27</obo:IAO_0000232>
<rdfs:label xml:lang="en">asymptomatic</rdfs:label>
Expand All @@ -3737,7 +3748,7 @@ Sagar Jain</obo:IAO_0000117>
<!-- http://purl.obolibrary.org/obo/OGMS_0000118 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000118">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ogms.owl#disease_stage"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000278"/>
<obo:IAO_0000115>A disease stage that marks the beginning of a disease</obo:IAO_0000115>
<obo:IAO_0000232>creation date 2018-11-27</obo:IAO_0000232>
<rdfs:label xml:lang="en">onset</rdfs:label>
Expand Down Expand Up @@ -3894,7 +3905,7 @@ Sagar Jain</obo:IAO_0000117>
<!-- http://purl.obolibrary.org/obo/OGMS_0000133 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OGMS_0000133">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/ogms.owl#disease_stage"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000278"/>
<rdfs:label>progression stage</rdfs:label>
</owl:Class>

Expand Down Expand Up @@ -4051,17 +4062,6 @@ Sagar Jain</obo:IAO_0000117>



<!-- http://purl.obolibrary.org/obo/ogms.owl#disease_stage -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/ogms.owl#disease_stage">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/BFO_0000015"/>
<obo:IAO_0000115>A part of a disease course</obo:IAO_0000115>
<obo:IAO_0000116 xml:lang="en">This class should be imported from OBI. https://github.com/OGMS/ogms/issues/105</obo:IAO_0000116>
<rdfs:label xml:lang="en">disease stage</rdfs:label>
</owl:Class>



<!--
///////////////////////////////////////////////////////////////////////////////////////
//
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