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@meghalithic meghalithic commented May 2, 2025

issue #3027

creating the following terms: facial crest, nasal notch, and staphylon

@meghalithic meghalithic requested a review from rays22 May 2, 2025 10:08
@github-actions github-actions bot requested a review from cmungall May 2, 2025 10:11
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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

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It looks like you inadvertently created two “facial crest” terms.

And the first one has logical axioms that can’t be represented in OBO.

@gouttegd gouttegd mentioned this pull request May 2, 2025
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gouttegd commented May 6, 2025

@meghalithic There are a lot of minor conflicts, likely due to the fact that the first commit of the PR was done nearly two years ago. Do you want me to resolve them for you?

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@gouttegd yes please! Thank you!

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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

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The conflicts have been fixed (which makes the changes much easier to review now that they are no longer interspersed with unrelated changes).

The logical definition of 'nasal notch' is problematic, see below.

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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

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Changes detected in src/ontology/uberon-edit.obo involving intersection_of. Review by specific Uberon Core Team member is required.

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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.

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KrishnaTO commented Jan 16, 2026

@matentzn Should be ready for rebase since all the reviews have been completed.

May encounter issue during rebasing replacing
property_value: has_ontology_root_term UBERON:0035943
with
owl-axioms: Prefix(owl:=<http://www.w3.org/2002/07/owl#>)\nPrefix...
but should ignore incoming, since similar code found only in various imports (https://github.com/search?q=org%3Aobophenotype+%22owl-axioms%3A+Prefix%22&type=code)

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This PR modifies some logical definitions. See details below:

Number of classes with modified logical definitions: 1

facial crest

No changes in inferred subclasses.

Replaced 'intersection_of' with 'is_a' for the facial crest term to correct its classification. Removed the accidentally added obsolete term 'Facial crest' (UBERON:8500008) for ontology cleanup.
Corrected the spelling of the synonym from 'nasoincisve notch' to 'nasoincisive notch' for UBERON:8500006 in the ontology file.
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I have made sure all of @gouttegd comments are implemented and will proceed to merge once QC has finished.

@matentzn matentzn merged commit b433e90 into master Jan 16, 2026
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6 participants