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Add "disease or disorder" to COB #226

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Add "disease or disorder" to COB #226

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a9d6104
Add "disease or disorder" to COB
matentzn Jan 26, 2023
4b73d2b
Add disease and disorder distinctions
matentzn Jan 30, 2023
a0161b6
Update cob-edit.owl
matentzn Jan 30, 2023
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73 changes: 72 additions & 1 deletion src/ontology/cob-edit.owl
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,8 @@
xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
xmlns:skos="http://www.w3.org/2004/02/skos/core#"
xmlns:terms="http://purl.org/dc/terms/">
xmlns:terms="http://purl.org/dc/terms/"
xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#">
<owl:Ontology rdf:about="http://purl.obolibrary.org/obo/cob/cob-edit.owl">
<owl:imports rdf:resource="http://purl.obolibrary.org/obo/cob/cob-annotations.owl"/>
<dc:description xml:lang="en">COB brings together key terms from a wide range of OBO projects to improve interoperability.</dc:description>
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<!-- http://purl.obolibrary.org/obo/IAO_0000119 -->

<owl:AnnotationProperty rdf:about="http://purl.obolibrary.org/obo/IAO_0000119"/>



<!-- http://purl.org/dc/elements/1.1/creator -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/creator"/>



<!-- http://purl.org/dc/elements/1.1/description -->

<owl:AnnotationProperty rdf:about="http://purl.org/dc/elements/1.1/description"/>
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<!-- http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym -->

<owl:AnnotationProperty rdf:about="http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym"/>



<!-- http://www.w3.org/2004/02/skos/core#exactMatch -->

<owl:AnnotationProperty rdf:about="http://www.w3.org/2004/02/skos/core#exactMatch"/>
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<obo:IAO_0000115>A process during which an organism comes into contact with another entity.</obo:IAO_0000115>
<rdfs:label xml:lang="en">exposure of organism</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/COB_0001100 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0001100">
<owl:equivalentClass>
<owl:Class>
<owl:unionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0001101"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/COB_0001102"/>
</owl:unionOf>
</owl:Class>
</owl:equivalentClass>
<rdfs:comment>This class groups the two defined classes &quot;disease&quot; and &quot;disorder&quot;. It supports use cases that conflate the two classes for pragmatic reasons.</rdfs:comment>
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Note, there is no useful way to define this class in a human readable way. But there is a very clear logical definition, which should satisfy any need for further definition.

<rdfs:label xml:lang="en">disease or disorder</rdfs:label>
<rdfs:seeAlso rdf:resource="https://github.com/OBOFoundry/COB/pull/226"/>
<rdfs:seeAlso>https://github.com/OBOFoundry/COB/issues/19</rdfs:seeAlso>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/COB_0001101 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0001101">
<obo:IAO_0000115>A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.</obo:IAO_0000115>
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@wdduncan suggests to make this a subclass of disposition in BFO. See related comment: https://github.com/OBOFoundry/COB/pull/226/files#r1090641271

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Hello Nico,
Looks like we have a resolution.
Three new terms in COB:
disease COB_0001101
disorder COB_0001102
disease or disorder COB_0001100. - which is a union of COB_0001101 and COB_0001102

One request, for the source of the disease definition, that it be the Disease Ontology, as we originally defined the term 'disease' which OGMS then adopted.
rdf:resource="http://purl.obolibrary.org/obo/doid.owl"/>

Cheers,
Lynn

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In OGMS, which is aligned with BFO, disease is defined as "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." This definition comes from PMID:21347182, "Toward an Ontological Treatment of Disease and Diagnosis," 2009, by Scheuermann, Ceusters, and Smith. This is original source of this definition (not DO).

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@matentzn My suggestion was to make it a subclass of COB:disposition, which (at present) has a BFO IRI.

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@matentzn see my comment here.

<dc:creator rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
<oboInOwl:hasRelatedSynonym>disorder</oboInOwl:hasRelatedSynonym>
<rdfs:label xml:lang="en">disease</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0001101"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.</owl:annotatedTarget>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
</owl:Axiom>



<!-- http://purl.obolibrary.org/obo/COB_0001102 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/COB_0001102">
<obo:IAO_0000115>A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.</obo:IAO_0000115>
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@wdduncan suggests to make this a subclass of material entity in BFO. Are you saying this @wdduncan because of the verbatim definitions here, or because you honestly believe that disorders are "material entities"? I thought this is exactly the problem with disease - that these terms have many aspects and therefore we should not just make them subclass of a specific BFO thing. Even @lschriml was contemplating they should be modelled as processes. I think we pretty much agreed that we wont agree on a BFO alignment for disease?

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@addiehl addiehl Jan 30, 2023 •
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In OGMS, which is aligned with BFO, disease is defined as "A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism." This definition comes from PMID:21347182, "Toward an Ontological Treatment of Disease and Diagnosis," 2009, by Scheuermann, Ceusters, and Smith. This is original source of this definition (not DO). This would be good reading for MONDO folks and other who are interested in the source of this debate.

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We have obviously read this

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(I know you have)

<dc:creator rdf:resource="https://orcid.org/0000-0002-7356-1779"/>
<rdfs:label xml:lang="en">disorder</rdfs:label>
</owl:Class>
<owl:Axiom>
<owl:annotatedSource rdf:resource="http://purl.obolibrary.org/obo/COB_0001102"/>
<owl:annotatedProperty rdf:resource="http://purl.obolibrary.org/obo/IAO_0000115"/>
<owl:annotatedTarget>A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.</owl:annotatedTarget>
<obo:IAO_0000119 rdf:resource="http://purl.obolibrary.org/obo/ogms.owl"/>
</owl:Axiom>
</rdf:RDF>


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