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.

[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.

[cellsemantic]

Reports relocated. ⚠️ The leaf template (hra-small-intestine.template.tsv) is empty — 0 new terms. This PR currently adds only reports, which don't belong in the ontology. Needs a decision: are any terms actually intended here, or should this PR be closed?

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Automated update (@cellsemantic / dragon-ai-agent, for @dosumis). Reports were relocated out of src/templates/ → bulk_ntr_workflow/outputs/<name>-reports/ to match the canonical layout (PR #3700). Note: the corrected reports-location docs currently live only on add-hra-muscular-ntr (#3700), not master. Batch-size policy for this HRA set: ≥20 new terms → ODK-register; <20 → hand-edit into uberon-edit.obo.

[ai4c-agent]

Claude finished @dosumis's task in 3m 30s —— View job

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

Task list

• Gather context and read latest comments (cellsemantic's relocation note + decision question)
• Check current diff vs base commit (post-relocation state, 9 files / +57)
• Verify no new terms/logical axioms are actually introduced
• Answer the "close vs keep" decision question
• Post final review + set PR review status

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Review Checklist

• Hierarchy and parents are consistent (N/A — no new logical axioms; templates are header-only)
• Definitions and supporting references look adequate (N/A — no new terms)
• Obsolete or replacement handling is safe — N/A, but see 🟡 report-consistency issue below
• OBO and ODK conventions appear preserved
• No obvious CI, auth, or workflow regression

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Answering the open question (cellsemantic, 2026-07-09)

Confirmed against the diff (git diff 4f80568...HEAD): src/templates/hra-small-intestine.template.tsv and -groups.template.tsv are header-only, 0 data rows. All 13 input rows resolved to one of: confirmed existing UBERON match, out-of-scope, or manual-curation — none produced a genuinely new term. Per the batch-size policy stated in this thread (<20 new terms → hand-edit into uberon-edit.obo; ≥20 → ODK-register), there is nothing to hand-edit here, because the count of actual new terms is zero.

Given that, this PR is legitimately a "no-op for the ontology, audit-trail only" PR — it doesn't touch uberon-edit.obo or any component the build consumes (empty ROBOT templates with no rows produce no axioms, and they're correctly not registered in uberon-odk.yaml). Recommendation: don't close it — merge it as a record of the pipeline run (matches precedent of other bulk_ntr_workflow report-only PRs), then handle the 2 manual_curation.tsv items (circular/longitudinal muscle, lamina propria/GALT split) as their own follow-up issue/PR with real term additions. Closing would just discard the curation work already done in the reports.

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Issues Found

🟡 IMPORTANT: Two source terms are double-counted across mutually-exclusive report files, breaking the documented QC invariant

Per bulk_ntr_workflow/CLAUDE.md: "Row counts: input − confirmed_match − out_of_scope − manual_curation = leaf + group". Here: 13 − 10 − 2 − 2 = −1, not 0 (leaf+group=0). The mismatch traces to:

• muscularis mucosa appears as confirmed_match in candidates.tsv:3 and as a rejected/misplaced entry in out_of_scope.tsv:2.
• circular/longitudinal muscle appears as possible_match in candidates.tsv:12 and in manual_curation.tsv:3 with overlapping-but-not-identical guidance.

Neither case is anatomically wrong on its own, but the reports are supposed to be a strict partition of the 13 input rows (that's what the PR description's "10 + 2 + 2" tally assumes, and what a curator scanning file-by-file would assume). A curator working strictly from manual_curation.tsv could act on circular/longitudinal muscle without realizing candidates.tsv already resolved it as possible_match: UBERON:0006660, or vice versa. Recommend either de-duplicating (each label should land in exactly one report) or, if intentionally cross-referenced, adding an explicit note in each file pointing to the other ("see also out_of_scope.tsv" / "see also candidates.tsv").

🔵 SUGGESTION (carried over, still unaddressed): empty table column in input.tsv

All 13 rows still have an empty table column despite small-intestine.csv having tables=small-intestine. Looks like a tables(CSV) → table(report) column-name mismatch in the generator script. Doesn't affect template output, but makes input.tsv less useful standalone.

🔵 SUGGESTION (carried over): add a uberon_label column to candidates.tsv

Several matches have a UBERON canonical label that differs from the source label (serosa→serous membrane, submucosal plexus of Meissner→submucous nerve plexus). Showing the canonical label alongside the ID would save curators a lookup.

🔵 SUGGESTION (resolved from prior review): ODK registration

Correctly deferred — templates are empty, so no registration is needed yet; this is fine as-is until real terms are added in a follow-up.

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Recommendation

No ontology risk (no axioms, no obsoletions, no ODK/build regression) — this should not be closed, it's useful provenance for a completed pipeline run with genuinely zero new terms. Requesting changes only for the 🟡 report double-counting issue, since it undermines the reliability of the audit trail that is this PR's entire content. Once that's cleaned up (or explicitly cross-referenced), this is mergeable.

[github-actions]

This PR modifies some logical definitions. See details below:

Number of classes with modified logical definitions: 1

gABAergic system

No changes in inferred subclasses.

[ai4c-agent]

Review Checklist

• Hierarchy and parents are consistent (N/A — no new logical axioms; templates are header-only)
• Definitions and supporting references look adequate (N/A — no new terms)
• Obsolete or replacement handling is safe — N/A, but see report-consistency issue below
• OBO and ODK conventions appear preserved
• No obvious CI, auth, or workflow regression

Re: "should this PR be closed?" — No. git diff 4f80568...HEAD confirms the leaf/groups templates are header-only (0 new terms), and per the stated batch-size policy (<20 new terms → hand-edit) there's nothing to hand-edit since the true new-term count is zero. This PR is a legitimate audit-trail-only record of a completed pipeline run and touches nothing the build consumes (no uberon-edit.obo changes, templates correctly unregistered in uberon-odk.yaml).

🟡 IMPORTANT: muscularis mucosa and circular/longitudinal muscle are each double-counted across mutually-exclusive report files (candidates.tsv vs out_of_scope.tsv; candidates.tsv vs manual_curation.tsv), which breaks the QC invariant documented in bulk_ntr_workflow/CLAUDE.md ("input − confirmed_match − out_of_scope − manual_curation = leaf + group": 13−10−2−2 = −1, not 0). A curator working from only one report file could act inconsistently. Please de-duplicate the categorization or add explicit cross-references between the files.

🔵 SUGGESTION (carried over, unaddressed): input.tsv's table column is empty for all 13 rows despite small-intestine.csv having tables=small-intestine — looks like a column-name mismatch in the generator.

🔵 SUGGESTION (carried over): add a uberon_label column to candidates.tsv for matches where the UBERON canonical label differs from the source label.

No ontology-level risk; requesting changes only to fix the report double-counting so this PR's audit trail is internally consistent before merge.