OBI with workshop-revised COB demo #1834
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Discussed on OBI dev call 2024-11-04: James will be updating the revised COB test PR to include "disposition", "site", and "function", plus some object properties and data properties, so that others can test a revised version of COB with those included. That will resolve these three dangling BFO classes in this demo. Jie proposed discussing the creation of a new OMO release in the next OBO call; a new OMO release would resolve the one remaining dangling BFO class, GDC. |
src/ontology/catalog-v001.xml
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| <?xml version="1.0" encoding="UTF-8" standalone="no"?> | |||
| <catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog"> | |||
| <uri id="Imports Wizard Entry" name="http://purl.obolibrary.org/obo/cob/releases/2024-10-24/cob.owl" uri="https://raw.githubusercontent.com/OBOFoundry/COB/f2782d893faa87a2a9de41a1884e849d8bf628b9/cob.owl"/> | |||
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@sebastianduesing Please try this again with my updates to OBOFoundry/COB#288
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Done; looks a lot better now.
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This PR is a version of the OBI-COB transition that uses the revised version of COB that implements the decisions made during the workshop (OBOFoundry/COB#288). It is very similar to the previous OBI-COB demo PRs I've created, with a handful of cosmetic differences (e.g., COB:'molecular entity' is now COB:'molecule', so CHEBI:'molecular entity' was obsoleted and replaced with COB:'molecule'), plus a couple non-trivial differences/issues that will require some further decision-making.
Namely, some BFO terms that were previously in COB were not discussed/decided upon during the workshop, including BFO:0000016 "disposition", BFO:0000029 "site", and BFO:0000034 "function". These classes are not in the revised version of COB at present, so for the time being, these are all dangling classes in this PR. I haven't touched any of their uses. To restore some core functionality, we'll need to either (1) redirect all uses of these terms away from them, as we've done for other BFO terms that we knew weren't going in COB, or (2) place these three BFO classes in COB.