Add kidney volume terms for GWAS Catalog

[Copilot]

Plan for Adding Kidney Volume Terms

• Investigate repository structure and patterns
• Identify the appropriate DOSDP pattern (entity_attribute.tsv)
• Verify UBERON IDs for anatomical structures
• Add three new OBA terms to entity_attribute.tsv
• Add UBERON:0006171 to merged_import.owl manually
• Regenerate patterns/definitions.owl with correct labels
• Verify all terms have proper definitions
• Run security checks
• Clean up tools/ directory from git tracking
• Normalize term placement - move new terms to end of file
• Final verification

Summary:
Successfully added three new kidney volume terms for GWAS Catalog:

1. OBA:2100000 - kidney sinus volume
2. OBA:2100001 - kidney medulla volume
3. OBA:2100002 - kidney cortex volume

All terms are now properly positioned at the end of entity_attribute.tsv file as requested.

Reference: PMID:41077127
Contributor: https://orcid.org/0000-0001-6757-4744

Original prompt

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This section details on the original issue you should resolve

<issue_title>NTR: kidney volume terms</issue_title>
<issue_description>New term requests for GWAS Catalog (kidney volume):

1- Kidney sinus volume
2- Kidney medulla volume
3- Kidney cortex volume

x-ref: PMID:41077127
orcid: https://orcid.org/0000-0001-6757-4744</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes NTR: kidney volume terms #409

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[ar-ibrahim]

@copilot Normalize newly added OBA terms so that the new term IDs are at the end of the entity_attribute.tsv file.

[Copilot]

@copilot Normalize newly added OBA terms so that the new term IDs are at the end of the entity_attribute.tsv file.

Done. The three new kidney volume terms (OBA:2100000, OBA:2100001, OBA:2100002) have been moved to the end of entity_attribute.tsv. Commit: 2f458e2

[aleixpuigb]

Copilot has added the Uberon import manually into merged_import instead of into uberon_terms.txt. ATM, it can't do that, so you need to do it manually. I suggest to remove the changes in the file and then add the import locally.

[aleixpuigb]

GO has obsoleted serine family amino acid metabolic process and 2 other terms.

[ar-ibrahim]

Yes I ran the QC locally and working on fixing the obsoletions. The PR is still a draft.