Add HRA small-intestine NTR batch outputs and review reports

[zhengj2007]

Generated via bulk_ntr_workflow from source_data/small-intestine.csv.

Pipeline completed through Stage 4:

• 13 input rows processed
• 0 new terms remained in final template after merge filtering
• 10 confirmed existing UBERON matches excluded
• 2 out-of-scope terms excluded
• 2 manual-curation entries flagged
• 4 name corrections reported

Adds the small-intestine source CSV, generated template stubs, and report TSVs (candidates, errors, input, manual_curation, name_corrections, out_of_scope).

[ai4c-agent]

Claude finished @zhengj2007's task in 4m 35s —— View job

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PR Review: Add HRA small-intestine NTR batch outputs and review reports

• Gather context and read PR description
• Review changed files (CSV, templates, reports)
• Check hierarchy and parent consistency
• Check definitions, xrefs, and references
• Verify OBO/ODK conventions
• Post final review summary

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Review Checklist

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

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Summary

This is a well-executed pipeline-output PR. All 13 HRA ASCTB small-intestine input terms have been processed; no new UBERON terms are introduced because every term either already exists, is out-of-scope, or requires manual curation before a new ID can be assigned. The report files are detailed and provide actionable curator guidance.

UBERON ID verification (spot-checked via obo-grep.pl):

Source label	Candidates UBERON	Actual name in ontology	Status
Epithelium	UBERON:0013636	epithelium of intestinal villus	✅ valid
muscularis mucosa	UBERON:0006676	muscularis mucosa	✅ exact
muscularis externa	UBERON:0006660	muscular coat	✅ valid synonym
muscularis propria	UBERON:0006660	muscular coat	✅ valid synonym
submucosal plexus of Meissner	UBERON:0005304	submucous nerve plexus	✅ valid (eponym)
myenteric plexus of Auerbach	UBERON:0002439	myenteric nerve plexus	✅ valid (eponym)
mucosa	UBERON:0000344	mucosa	✅ exact
submucosa	UBERON:0000009	submucosa	✅ exact
serosa	UBERON:0000042	serous membrane	✅ valid synonym
connective tissue	UBERON:0002384	connective tissue	✅ exact

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Issues Found

🟡 IMPORTANT: Stage 5 (ODK registration) not completed

hra-small-intestine.template.tsv and hra-small-intestine-groups.template.tsv are not registered in src/ontology/uberon-odk.yaml. The existing hra-skeleton template is registered (line 177). Since both templates are currently empty (header-only, no new terms), omitting registration is reasonable for now — but when terms are eventually added via manual curation, registration will be required before the ODK build will include them. This should be done in the follow-up PR that adds the actual terms.

🟡 IMPORTANT: "muscularis propria" and "muscularis externa" both map to UBERON:0006660

Two distinct source terms map to the same UBERON ID (muscular coat). While anatomically valid — these are accepted synonyms — the candidates.tsv report doesn't explicitly flag the duplication. A curator reviewing the report could mistake this for a pipeline error. Consider adding a note such as "muscularis propria is a synonym for muscularis externa; both map to UBERON:0006660 (muscular coat)".

🔵 SUGGESTION: Empty table column in input.tsv

All 13 rows have an empty table column in input.tsv despite the source CSV having "small-intestine" in the tables column. This looks like a column-name mismatch (tables in CSV → table in report). Minor pipeline issue — does not affect the template output.

🔵 SUGGESTION: UBERON canonical labels not shown in candidates.tsv

For matches where the UBERON primary label differs from the source label (e.g., "serosa" → "serous membrane", "submucosal plexus of Meissner" → "submucous nerve plexus"), the candidates report shows only the UBERON ID without the canonical label. Including the UBERON label in a uberon_label column would help curators verify matches without additional lookups.

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Manual Curation Quality

The two manual-curation entries are well-documented:

• "circular/longitudinal muscle" — correctly identified as non-standard notation; recommends either splitting into separate NTRs for the circular/longitudinal layers (referencing UBERON:0012368, UBERON:0012369) or mapping to existing UBERON:0006660.
• "Lamina propria/Gut associated lymphoid tissue (GALT)" — correctly identifies the slash notation as conflating two distinct structures (UBERON:0000030, UBERON:0001962) and proposes either splitting into two NTRs or creating "lamina propria of intestinal villus" with a proper intersection_of axiom.

Both suggestions follow UBERON design patterns appropriately.

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Recommendation

This PR is ready to merge. The report files accurately document the pipeline run, the UBERON ID mappings are correct, and the flagged items provide clear curator guidance. The 🟡 issues above are follow-up items, not blockers: ODK registration belongs in the term-addition PR, and the duplicate-mapping note is documentation polish.

[ai4c-agent]

Well-executed pipeline output PR. All 13 HRA ASCTB small-intestine input terms correctly processed — 10 confirmed matches verified against uberon-edit.obo, 2 out-of-scope terms properly flagged with detailed anatomical reasoning, and 2 manual-curation entries well-documented with specific UBERON term references and actionable suggestions. No new terms added; the templates are empty header stubs pending manual curation follow-up. Two 🟡 notes for follow-up PRs: (1) ODK registration of the new templates should happen when terms are eventually added; (2) candidates.tsv could note that 'muscularis propria' and 'muscularis externa' are synonyms both mapping to UBERON:0006660 to avoid curator confusion.