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add disjoint union of to 'disease characteristic' subclasses #8766

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add disjoint union of to 'disease characteristic' subclasses #8766

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3ab4a4f
add disjoint union of to 'disease characteristic' subclasses
nicolevasilevsky Feb 22, 2025
b8a3ffe
add disjoint union of axiom
nicolevasilevsky Feb 22, 2025
cad65c7
add disjoint union of axiom to 'congenital or acquired'
nicolevasilevsky Feb 22, 2025
78c17a9
add disjoint union of axioms to disease characteristic classes
nicolevasilevsky Feb 22, 2025
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16 changes: 16 additions & 0 deletions docs/editors-guide/f-entities.md
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Original file line number Diff line number Diff line change
Expand Up @@ -227,3 +227,19 @@ If you make changes to a Mondo term based on requests on a GitHub ticket, please
## Susceptibility terms

Susceptibility to diseases should be classified under MONDO:0042489 'disease susceptibility' (or MONDO:0020573 'inherited disease susceptibility', as appropriate). We should group any OMIM susceptibility terms under a susceptibility to disease term. We will not add OMIM xrefs to these, even if the term is part of the OMIMPS. For example, https://www.omim.org/phenotypicSeries/PS161400 - we will create a new class called narcolepsy, susceptibility but will NOT refer back to the OMIMPS. (See related ticket: [https://github.com/monarch-initiative/mondo/issues/5511](https://github.com/monarch-initiative/mondo/issues/5511)).

## Disease characteristic

MONDO:0021125 disease characteristic describes attributes of a disease and these terms are used in logical axioms in Mondo.

To add a Disjoint Union Of axiom to disease characteristic terms, follow the instructions below:
1. In Protege, select the term (eg 'classic or non-classic genetic disease presentation')
2. In the Description box, click the + next to the 'Disjoint Union Of' axiom
3. Click the Expression editor tab
4. Create a commna separated list of the terms that are subclasses of the class (eg 'classic presentation', 'non-classic presentation')
5. Click OK
6. Move the axiom to the 'axioms' file. Click on the new axiom that you created (so it is highlighted in blue)
7. Right click and select move axiom(s) to ontology
8. Select an ontology: axioms
9. Click OK
10. Save the file and commit
191 changes: 184 additions & 7 deletions src/ontology/imports/axioms.owl
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Expand Up @@ -77,6 +77,23 @@



<!-- http://purl.obolibrary.org/obo/HP_0031690 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/HP_0031690"/>



<!-- http://purl.obolibrary.org/obo/MONDO_0021126 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0021126">
<owl:disjointUnionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0021127"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0021128"/>
</owl:disjointUnionOf>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MONDO_0021127 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0021127"/>
Expand All @@ -89,6 +106,46 @@



<!-- http://purl.obolibrary.org/obo/MONDO_0021135 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0021135">
<owl:disjointUnionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0021136"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0021137"/>
</owl:disjointUnionOf>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MONDO_0021136 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0021136"/>



<!-- http://purl.obolibrary.org/obo/MONDO_0021137 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0021137"/>



<!-- http://purl.obolibrary.org/obo/MONDO_0021139 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0021139">
<owl:disjointUnionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0021140"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0021141"/>
</owl:disjointUnionOf>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MONDO_0021140 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0021140"/>



<!-- http://purl.obolibrary.org/obo/MONDO_0021141 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0021141"/>
Expand All @@ -101,6 +158,103 @@



<!-- http://purl.obolibrary.org/obo/MONDO_0022202 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0022202"/>



<!-- http://purl.obolibrary.org/obo/MONDO_0045034 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0045034">
<owl:disjointUnionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/HP_0031690"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0045036"/>
</owl:disjointUnionOf>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MONDO_0045036 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0045036"/>



<!-- http://purl.obolibrary.org/obo/MONDO_0045040 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0045040">
<owl:disjointUnionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0022202"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0045042"/>
</owl:disjointUnionOf>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MONDO_0045042 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0045042"/>



<!-- http://purl.obolibrary.org/obo/MONDO_0100355 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0100355">
<owl:disjointUnionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0100356"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0100357"/>
</owl:disjointUnionOf>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MONDO_0100356 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0100356"/>



<!-- http://purl.obolibrary.org/obo/MONDO_0100357 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0100357"/>



<!-- http://purl.obolibrary.org/obo/MONDO_0100369 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0100369">
<owl:disjointUnionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0100426"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0100427"/>
</owl:disjointUnionOf>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MONDO_0100426 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0100426"/>



<!-- http://purl.obolibrary.org/obo/MONDO_0100427 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0100427"/>



<!-- http://purl.obolibrary.org/obo/MONDO_0700004 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0700004">
<owl:disjointUnionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0700005"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0700006"/>
</owl:disjointUnionOf>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MONDO_0700005 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0700005"/>
Expand All @@ -113,6 +267,29 @@



<!-- http://purl.obolibrary.org/obo/MONDO_0700061 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0700061">
<owl:disjointUnionOf rdf:parseType="Collection">
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0700062"/>
<rdf:Description rdf:about="http://purl.obolibrary.org/obo/MONDO_0700063"/>
</owl:disjointUnionOf>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/MONDO_0700062 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0700062"/>



<!-- http://purl.obolibrary.org/obo/MONDO_0700063 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/MONDO_0700063"/>



<!-- http://purl.obolibrary.org/obo/SO_0000704 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/SO_0000704"/>
Expand Down Expand Up @@ -142,14 +319,14 @@
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MONDO_0021127"/>
<owl:disjointWith rdf:nodeID="genid4"/>
<owl:disjointWith rdf:nodeID="genid22"/>
</owl:Restriction>
</owl:annotatedSource>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#disjointWith"/>
<owl:annotatedTarget rdf:nodeID="genid4"/>
<owl:annotatedTarget rdf:nodeID="genid22"/>
<oboInOwl:created_by>cjm</oboInOwl:created_by>
</owl:Axiom>
<owl:Restriction rdf:nodeID="genid4">
<owl:Restriction rdf:nodeID="genid22">
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MONDO_0021128"/>
</owl:Restriction>
Expand All @@ -168,20 +345,20 @@
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MONDO_0700005"/>
<owl:disjointWith rdf:nodeID="genid9"/>
<owl:disjointWith rdf:nodeID="genid27"/>
</owl:Restriction>
</owl:annotatedSource>
<owl:annotatedProperty rdf:resource="http://www.w3.org/2002/07/owl#disjointWith"/>
<owl:annotatedTarget rdf:nodeID="genid9"/>
<owl:annotatedTarget rdf:nodeID="genid27"/>
<oboInOwl:created_by>https://orcid.org/0000-0002-4142-7153</oboInOwl:created_by>
</owl:Axiom>
<owl:Restriction rdf:nodeID="genid9">
<owl:Restriction rdf:nodeID="genid27">
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/RO_0000053"/>
<owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/MONDO_0700006"/>
</owl:Restriction>
</rdf:RDF>



<!-- Generated by the OWL API (version 4.5.26.2023-07-17T20:34:13Z) https://github.com/owlcs/owlapi -->
<!-- Generated by the OWL API (version 4.5.29.2024-05-13T12:11:03Z) https://github.com/owlcs/owlapi -->