Adding gross anatomical part. Fixes #2921

[cmungall]

To align with COB

See

• Replace CARO IDs in cob-non-native OWL export OBOFoundry/COB#248

[cmungall]

Unsatisfiable - Joeys are not substances

[cmungall]

This is turning out to be harder than I expected

[gouttegd]

Unsatisfiable - Joeys are not substances

We have encountered this one before, and it was agreed that the

'median vaginal canal' SubClassOf: 'channel for' some embryo

axiom should be removed, but then there was no follow-up…

Edit: My bad, I’ve just seen that you did exactly that in the subsequent commit. Sorry for the noise.

[gouttegd]

Regarding the last QC failure, I believe you have run into what should be considered a bug in the ODK. I have opened an issue with the details on the ODK repo.

A quick (but crude) workaround until the issue is fixed in the ODK would be to edit the standard Makefile to change the definition of $(SRCMERGED) from

SRCMERGED     = $(TMPDIR)/merged-$(SRC)

into

SRCMERGED     = $(TMPDIR)/merged-uberon-edit.ofn

to force the intermediate file on which the ROBOT report command is run to be written in OFN rather than OBO format, thereby avoiding OBO serialisation quirks.

[github-actions]

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR creator will be allowed to proceed with merging without explicit approval, should they wish to do so.

[KrishnaTO]

commit 1a338fe resolves review in #3151

[Copilot]

Pull request overview

This pull request adds a new high-level ontology term "gross anatomical part" (UBERON:0000001) to align with the Common Anatomy Reference Ontology (CARO) and COB standards. The term represents anatomical structures that are part of multicellular organisms at the gross anatomical level (above the cellular level).

Changes:

• Added new term UBERON:0000001 (gross anatomical part) with definition, cross-references, and relationships
• Reparented five existing terms to be children of the new gross anatomical part term instead of their previous parent terms
• Removed one relationship from the median vaginal canal term (appears unrelated to the PR's stated purpose)

[matentzn]

This was already added in COB with a COB id, I guess this PR complements it?

https://www.ebi.ac.uk/ols4/ontologies/cob/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_0001062?lang=en

[matentzn]

This looks good to me. I note that the COB definition of the same term is slightly different