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Reinstate Uberon terms in HCAO #109

Open paolaroncaglia opened 2 years ago

paolaroncaglia commented 2 years ago

While doing the last HCAO release on April 19th, Zoë noted that "there was an issue with UBERON_0039176 in the HCAO release - I don’t seem to be able to find this term anywhere, so not sure what it was, but I’ve removed it (possibly temporarily) from imports in order for the release to go through". Looking at the latest release of Uberon in Protege, UBERON_0039176 is 'subarachnoid space of spinal cord'. The term was created in July 2021. The 'subarachnoid space' branch was edited since the last HCAO release, but as far as I can see, UBERON_0039176 was unchanged, including its FMA xrefs. So, I'm not sure what the problem is. The sibling of UBERON_0039176 (UBERON_0039175) is in HCAO as expected. At the time of writing, the Uberon version containing the latest edits hasn't been updated in OLS yet: could that be the problem?

dosumis commented 2 years ago

Zoe still investigating.

paolaroncaglia commented 2 years ago

@zoependlington adding you as an assignee to record your work on this - thank you!

paolaroncaglia commented 2 years ago

Update: this issue is still unresolved. Zoë will continue to investigate before the next HCAO release.

zoependlington commented 2 years ago

There are now more terms that have the same issue. Comparing old version of the import, hcao.owl and the new version I genuinely can not see any difference so I am not sure why this issue is happening. Here are the new terms with issues that I have had to remove in order to do the release:

2022-06-10 13:35:48,116 ERROR org.obolibrary.robot.ReasonerHelper - unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0035074 2022-06-10 13:35:48,116 ERROR org.obolibrary.robot.ReasonerHelper - unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0000382 2022-06-10 13:35:48,116 ERROR org.obolibrary.robot.ReasonerHelper - unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0002297 2022-06-10 13:35:48,116 ERROR org.obolibrary.robot.ReasonerHelper - unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0034762 2022-06-10 13:35:48,116 ERROR org.obolibrary.robot.ReasonerHelper - unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0018232 2022-06-10 13:35:48,116 ERROR org.obolibrary.robot.ReasonerHelper - unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0014393 2022-06-10 13:35:48,116 ERROR org.obolibrary.robot.ReasonerHelper - unsatisfiable: http://purl.obolibrary.org/obo/UBERON_0013228

dosumis commented 2 years ago

Should be fixed by https://github.com/ebi-ait/ontology/pull/4/files

amnonkhen commented 2 years ago

included in 1.0.38: [ebi-ait/hca-ebi-dev-team#490]