Fix BFO incompatibility #709
Conversation
Replace custom definitions in some BFO classes by their original (upstream-defined) versions. Move the custom definitions into comments instead. This avoids trigerring the "multiple definitions" QC violation when one needs to import both RO (and the included BFO "minimal classes" subset) and the upstream-provided BFO.
Make sure the BFO components (bfo-classes-minimal.owl and bfo-axioms.owl) are imported into the -edit file, as they used to be (indirectly, through ro-core) prior to the ODK migration.
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@gouttegd Thanks for updating the definitions. I noticed that the editor notes and examples of usage are not being pulled into the component/import. E.g., see [material entity()https://ontobee.org/ontology/BFO?iri=http://purl.obolibrary.org/obo/BFO_0000040) on Ontobee. However, I think it would be helpful include the |
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There are many annotations mismatches that are breaking things. I don't know what the right way to fix all these are. I didn't implement the annotation qc checks that are causing issues (e.g., dc vs dcterms). |
This is another way of fixing #107, as an alternative to #707.
It keeps the manually curated copy of BFO (as components
bfo-classes-minimal.owlandbfo-axioms.owl), but updates the definitions on some the classes to match the definitions used in the version of BFO that is published atpurl.obolibrary.org/obo/bfo.owl, so as to avoid clashing definitions when importing RO and BFO in the same ontology. Original definitions in thebio-classes-minimal.owlcomponent are turned into comments.This is the least intrusive way of fixing #107.
The BFO components are also properly imported into the -edit file.