Add HRA kidney NTR template (2 new terms)

[zhengj2007]

Generated via bulk_ntr_workflow from source_data/kidney.csv:

• 2 new UBERON terms (UBERON:8930105-8930106)
  • kidney lymphatic vessel
  • epithelium of tip of renal papilla
• 0 parent-mapping errors (all source parents were UBERON IDs)
• 0 confirmed existing matches, 0 out-of-scope, 0 manual curation
• 1 name correction applied: 'Papillary Tip Epithelium' ->
  'epithelium of tip of renal papilla'

Note: kidney lymphatic vessel includes PMID:24065628; papillary tip epithelium still needs curator-supplied PMID/DOI beyond ASCTB/Wikipedia references.

[ai4c-agent]

Claude finished @zhengj2007's task in 3m 55s —— View job

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PR Review — Add HRA Kidney NTR Template (2 New Terms)

Checklist:

• Hierarchy and parents are consistent
• Definitions and supporting references look adequate (with one gap — see below)
• Obsolete or replacement handling is safe (N/A — no obsoletions)
• OBO and ODK conventions appear preserved
• No obvious CI, auth, or workflow regression

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Todo List:

• Gather context and read changed files
• Check parent terms for hierarchy consistency
• Verify term definitions and references
• Check OBO/ODK conventions
• Review checklist and post final review

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Summary

Two new terms are proposed for the HRA kidney atlas:

ID	Label	is_a	part_of
UBERON:8930105	kidney lymphatic vessel	UBERON:0001473 (lymphatic vessel)	UBERON:0002113 (kidney)
UBERON:8930106	epithelium of tip of renal papilla	UBERON:0000483 (epithelium)	UBERON:0009095 (tip of renal papilla)

Both IDs fall within the allocated range [8930000, 8931000) in uberon-idranges.owl. Neither term duplicates an existing UBERON entry. Parent terms all exist and are valid.

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Issues Found

🔴 CRITICAL — Templates not registered in uberon-odk.yaml

src/templates/hra-kidney.template.tsv and src/templates/hra-kidney-groups.template.tsv are not registered as components in src/ontology/uberon-odk.yaml. Comparing against the existing skeleton registration:

# in uberon-odk.yaml (existing pattern)
- filename: hra_skeleton.owl
  use_template: true
  templates:
    - hra-skeleton.template.tsv

Without equivalent entries for hra_kidney.owl and hra_kidney_groups.owl, the ODK build will never process these templates and the two terms will never appear in the generated ontology. The bulk_ntr_workflow/CLAUDE.md describes a Stage 5 (register_templates.py) precisely for this purpose. Please run that script or add the entries manually before merging.

Fix this →

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🟡 IMPORTANT — epithelium of tip of renal papilla lacks a real literature reference

The def_xref for UBERON:8930106 is:

https://purl.org/ccf/ASCTB-TEMP_papillary-tip-epithelium

This is only an ASCTB placeholder IRI — not a citable reference. Per the NTR workflow QC checklist (bulk_ntr_workflow/CLAUDE.md): "Every term has a real PMID/DOI (or ISBN) in def_xref — ASCTB-TEMP placeholder IRIs do not count as references."

The PR description already flags this as a known gap. A PMID should be added before or shortly after merging. Candidate papers cover urothelium/transitional epithelium of the renal papilla, e.g. work on the papillary surface epithelium in the context of reflux nephropathy or urothelial anatomy.

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🔵 SUGGESTION — Parent mismatch between source and template (documentation)

The input.tsv source lists UBERON:0006544 (kidney vasculature) as the parent for kidney lymphatic vessel, but the template correctly uses a genus-differentia decomposition: is_a lymphatic vessel + part_of kidney. This is the right ontological choice, but the divergence from the source parent is not documented. Consider adding a brief note (or ensuring the ASCTB source IRI in def_xref is sufficient traceability).

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🔵 SUGGESTION — Original source name not captured as synonym

name_corrections.tsv says:

Papillary Tip Epithelium → epithelium of tip of renal papilla — Keep source name as synonym.

The leaf template has no synonym column, so "Papillary Tip Epithelium" is not recorded as a synonym in the generated term. Consider adding a related_synonym or broad_synonym annotation for "papillary tip epithelium" either via a ROBOT template column extension or directly in uberon-edit.obo after import.

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What looks good

• Aristotelian definitions are well-formed and anatomically accurate.
• PMID:24065628 is cited for kidney lymphatic vessel (covers renal lymphatic anatomy).
• UBERON:0009095 (tip of renal papilla) is a valid parent; the epithelium of tip of renal papilla definition text accurately describes the urothelial transition zone.
• Name correction from "Papillary Tip Epithelium" → "epithelium of tip of renal papilla" follows UBERON naming conventions.
• Contributor ORCID, date, taxon, and HRA subset annotations are all present.
• No errors or unresolvable parent mappings.

[ai4c-agent]

Two new terms are well-formed and anatomically appropriate, but the PR has one blocker before merge:

🔴 CRITICAL: hra-kidney.template.tsv and hra-kidney-groups.template.tsv are not registered in src/ontology/uberon-odk.yaml. Without entries analogous to the existing hra_skeleton.owl component, the ODK build will never process these templates and the terms will not appear in the generated ontology. Run bulk_ntr_workflow/scripts/register_templates.py --name hra-kidney (or add entries manually) before merging.

🟡 IMPORTANT: epithelium of tip of renal papilla (UBERON:8930106) has only an ASCTB-TEMP placeholder IRI as its def_xref — a real PMID/DOI is required per the NTR workflow QC checklist.

See the full review comment for details and fix links.