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evoinfo / cdao

Comparative Data Analysis Ontology - A formalization of concepts and relations relevant to evolutionary comparative analysis
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deprecate the part_of property and consolidate its usages on belongs_to #21

Open balhoff opened 7 months ago

balhoff commented 7 months ago

This issue is motivated by achieving conformance with the OBO dashboard. In the near future, lack of conformance with the dashboard checks will impact an ontology's listing on the OBO homepage.

One of the failures is usage of an object property (part_of) with the same label as one found in RO. OBO ontologies should reuse RO properties whenever possible. In this case, CDAO actually contains another property stated to be equivalent to part_of: belongs_to. This situation isn't really encouraged either.

So I propose that we deprecate part_of, and rewrite any axioms using that property to instead use belongs_to. This should all be logically equivalent. Down the road we can remove the equivalence statement. This plan of action resolves the name conflict with RO, and simplifies the equivalent property situation. Farther down the road we could choose to adopt appropriate RO properties directly.

balhoff commented 7 months ago

This change was implemented in 081f2e49fe4c5bd8da3337e5207ffa94851bc5a3, as part of #20.

hlapp commented 7 months ago

Thanks Jim. If I understand correctly, then the change in #20 only rewrites axioms using CDAO:part_of to instead use CDAO:belongs_to, which were already asserted as equivalent. Indeed this should therefore not change any reasoning results.

This would, however, not yet resolve the name conflict with RO, right? I.e., accomplishing that is part of the downstream plan of action, not of the changeset in #20, correct? I suppose the deprecation, which is included in #20, is the second step, with the third step being removal?

balhoff commented 7 months ago

This would, however, not yet resolve the name conflict with RO, right? I.e., accomplishing that is part of the downstream plan of action, not of the changeset in #20, correct? I suppose the deprecation, which is included in #20, is the second step, with the third step being removal?

I wasn't clear about that part: per standard OBO deprecation procedure, I changed the rdfs:label for http://purl.obolibrary.org/obo/CDAO_0000194 from 'part_of' to 'obsolete part_of'. This eliminates the name conflict with RO. I left the equivalence axiom for now, to avoid reasoning impacts, but the final step would be removing that axiom. But then the deprecated term would be left in the ontology forever.