Uberon release 2024-10-31

[aleixpuigb]

DO NOT MERGE!

[github-actions]

Here's a diff of how this release impacts uberon-base.owl

[aleixpuigb]

Many terms are being classified as SubclassOf 'protein-containing material entity', which has been obsoleted in PRO. Probably is best to fix this before running the release, what do you think? @dosumis @gouttegd @cmungall

[dosumis]

It's obsolete in PRO https://www.ebi.ac.uk/ols4/ontologies/pr/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FPR_000050567

So should be possible to fix by fixing import.

@gouttegd - Assume we are now using base imports so we shouldn't be getting this indirectly?

[gouttegd]

@dosumis We are using base imports, but that didn’t help here because the faulty axioms seem to come directly from PR itself. I just tried refreshing my local PR mirror here, and it does not contain the deprecation axiom for PR:000050567, and to the contrary it contains many SubClassOf axioms that refers to PR:000050567 as the superclass, as if the entity had never been deprecated. Maybe something wrong happened on the PR side, I don’t know.

[gouttegd]

the faulty axioms seem to come directly from PR itself.

Correction: the faulty axioms come from the OBO PR slim, not from PR itself -- we do not import PR directly as it is too big.

The last release of the OBO PR slim does contain the faulty PR:000050567 axioms, while the current version of PR available on http://purl.obolibrary.org/obo/pr.owl (dated 8 August) does not, so I am not sure what happened. Possibly the last OBO PR slim was somehow made from an older version of PR, I don’t know.

[gouttegd]

I’ve made a PR to refresh the OBO PR slim. Once merged, refreshing the imports once again in Uberon should clear the issue.

[aleixpuigb]

Thank you @gouttegd, I will close this PR and refresh the imports. Once it is done I will run again the release.