add hra brain terms

[zhengj2007]

No description provided.

[ai4c-agent]

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

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PR Review: add hra brain terms

Review checklist:

• Hierarchy and parents are consistent
• Definitions and supporting references look adequate
• Obsolete or replacement handling is safe
• OBO and ODK conventions appear preserved
• No obvious CI, auth, or workflow regression

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Overview

This PR adds 12 new HRA (Human Reference Atlas) brain terms via ROBOT template (src/templates/hra-brain.template.tsv), along with the bulk NTR workflow intermediate files (JSON definitions, report TSVs). The workflow correctly identified and excluded 4 confirmed existing terms (amygdaloid complex, septal nuclei, thalamus, occipitotemporal fusiform gyrus occipital part) and correctly excluded 2 unresolvable terms (ifj1, ifj2) that need clarification from the ASCTB data providers.

However, there are several issues that need to be resolved before this can be merged.

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🔴 CRITICAL

1. UBERON_9920004 has [PENDING] definition and empty hierarchy (src/templates/hra-brain.template.tsv, line 5)

"cingulate gyrus, retrospleninal part" was not fully processed — the template row has [PENDING] as the definition and empty is_a/part_of columns. This violates QC checklist item 1 ("No [PENDING] definitions remain"). The term cannot be loaded by ROBOT.

The JSON subagent output (bulk_ntr_workflow/outputs/definitions/uberon_0002967.json) does have a resolution:

• Definition: "A subdivision of the cingulate gyrus located in its posterior-most region, corresponding to the retrosplenial cortical areas and comprising Brodmann areas 26, 29, and 30."
• is_a: UBERON:0000200 (gyrus)
• part_of: UBERON:0002967 (cingulate gyrus)
• def_xref: PMID:17572666
• xref: Wikipedia:Retrosplenial_cortex

These values need to be applied to the template row before merge. Fix this →

2. Typo in term name (src/templates/hra-brain.template.tsv, line 5)

cingulate gyrus, retrosplen**in**al part → should be cingulate gyrus, retrosplen**i**al part. The JSON output file (uberon_0002967.json) has the correct spelling "retrosplenial". This typo is present throughout the template (label column) and the bulk_ntr_workflow/outputs/definitions/input/uberon_0002967.json and src/templates/hra-brain-reports/input.tsv files. Fix this →

3. Three terms lack real literature references in def_xref (QC checklist item 2: "Every term has a real PMID/DOI — ASCTB-TEMP placeholder IRIs do not count"):

Term	ID	Current def_xref
extended amygdala	UBERON_9920005	ASCTB-TEMP IRI only
occipitoparietal transition region	UBERON_9920015	ASCTB-TEMP IRI only
occipitotemporal transition region	UBERON_9920017	ASCTB-TEMP IRI only

Suggested references:

• extended amygdala: PMID:25899707 (cited in related manual_curation.tsv for IFJ; a dedicated extended amygdala reference such as PMID:12948448 should be verified)
• occipitoparietal transition region: JSON unresolvable section suggests PMID:25316338 or PMID:28981612
• occipitotemporal transition region: JSON suggests PMID:19457377

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🟡 IMPORTANT

4. Possible overlap with existing UBERON:0013531 (retrosplenial region) — curator decision needed

The candidates.tsv flags "cingulate gyrus, retrosplenial part" as a possible_match for UBERON:0013531. Both terms cover the same Brodmann areas (26, 29, 30) and the same anatomical territory. The candidates report notes:

"UBERON:0013531 (retrosplenial region) refers to the same anatomical location but is classified as a cortical region (is_a: regional part of brain, part_of: cingulate cortex), while the requested term would be a gyral subdivision (is_a: gyrus, part_of: cingulate gyrus). Similar dual gyrus/cortex terminology exists in UBERON for anterior cingulate gyrus (UBERON:0002756) vs anterior cingulate cortex (UBERON:0009835)."

This is the correct reasoning for allowing both terms. However, the PR should document this decision, and the new term should add an xref or relationship to UBERON:0013531 for disambiguation.

5. ifj1 and ifj2 remain unresolved — labels are not anatomically standard

These are correctly excluded from the final template (good), but they are still present in the source data (hra-brain-reports/errors.tsv). Per the manual_curation.tsv, the ASCTB data providers need to clarify what anatomical/functional features distinguish ifj1 from ifj2, and provide standard anatomical names. Should be tracked as a follow-up action.

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🔵 SUGGESTIONS

6. ifs1–ifs4 source labels not retained as synonyms

The name_corrections.tsv recommends keeping the source labels (ifs1, ifs2, ifs3, ifs4) as exact synonyms since these are atlas-specific codes. The template currently only shows the corrected names (anterior/middle-anterior/middle-posterior/posterior inferior frontal sulcus) with no synonym column. Consider adding these as exact_synonym for atlas-to-ontology mapping.

7. PR has no description

The PR body is empty. A brief description of what terms are added, what was excluded and why, and what decisions were made during curation would aid review significantly.

8. bulk_ntr_workflow/ intermediate files

These files appear to be workflow artifacts (JSON inputs/outputs, initial TSVs). It's worth confirming whether these should be committed to the repository long-term or are only needed during the curation workflow.

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Summary

Verdict: Request changes. The template has an incomplete entry (UBERON_9920004 with [PENDING] definition and no hierarchy) and a typo in the same term's name, plus three terms without real literature references — all failing the QC checklist required before merge. The rest of the new terms (atrium of lateral ventricle, body/head of hippocampus, frontomarginal gyrus, extended amygdala, 4 inferior frontal sulcus subdivisions, 2 transition regions) look anatomically reasonable and well-structured.

[ai4c-agent]

This PR adds 12 new HRA brain terms but has several issues blocking merge:

🔴 CRITICAL:

1. UBERON_9920004 'cingulate gyrus, retrosplenial part' has a [PENDING] definition and empty is_a/part_of hierarchy — cannot be loaded by ROBOT. The resolved values exist in bulk_ntr_workflow/outputs/definitions/uberon_0002967.json and need to be applied to the template.
2. Typo in term name: 'retrospleninal' → 'retrosplenial' throughout.
3. Three terms (extended amygdala, occipitoparietal transition region, occipitotemporal transition region) have only ASCTB-TEMP placeholder IRIs as def_xref — real PMIDs/DOIs required per QC checklist.

🟡 IMPORTANT:
4. UBERON_9920004 possible overlap with existing UBERON:0013531 (retrosplenial region) — curator decision should be documented and a cross-reference added.
5. ifj1/ifj2 correctly excluded but need follow-up with ASCTB data providers for proper naming.

🔵 SUGGESTIONS:
6. ifs1–ifs4 source labels should be retained as exact synonyms.
7. PR needs a description explaining what was added, excluded, and why.

See detailed review in the PR comment.

[RiveraAndrea83]

Had a look on terms. Some are also present in HOMBA and well characterised: see https://alleninstitute.github.io/CCF-MAP/docs/HOMBA_ontology_v1.html

Others such as ifs1-4 are not used and I would not include them at this stage. There are also other terms that do not have really good supporting evidence and are transition zones between two different regions.

[ai4c-agent]

Claude finished @dosumis's task in 3m 35s —— View job

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PR Review: add hra brain terms (re-review after new commit)

Review checklist:

• Hierarchy and parents are consistent
• Definitions and supporting references look adequate
• Obsolete or replacement handling is safe
• OBO and ODK conventions appear preserved
• No obvious CI, auth, or workflow regression

---

What changed since the last review

The only new commit (877206a) moves report artifacts (candidates.tsv, errors.tsv, input.tsv, manual_curation.tsv, name_corrections.tsv) from src/templates/hra-brain-reports/ to bulk_ntr_workflow/outputs/hra-brain-reports/. This addresses SUGGESTION #8 from the previous review (artifact location), but none of the CRITICAL or IMPORTANT content issues from the prior review have been resolved — src/templates/hra-brain.template.tsv is byte-for-byte unchanged in its data rows.

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🔴 CRITICAL (unresolved from previous review)

1. UBERON_9920004 still has [PENDING] definition and empty hierarchy (src/templates/hra-brain.template.tsv, line 5)

http://purl.obolibrary.org/obo/UBERON_9920004	cingulate gyrus, retrospleninal part	[PENDING]	...	(is_a and part_of columns empty)

This violates the workflow's own QC checklist (bulk_ntr_workflow/CLAUDE.md): "No [PENDING] definitions remain." ROBOT cannot load this row as-is. The resolved values already exist in bulk_ntr_workflow/outputs/definitions/uberon_0002967.json:

• Definition: "A subdivision of the cingulate gyrus located in its posterior-most region, corresponding to the retrosplenial cortical areas and comprising Brodmann areas 26, 29, and 30."
• is_a: UBERON:0000200 (gyrus) — verified active, not obsolete
• part_of: UBERON:0002967 (cingulate gyrus) — verified active, not obsolete
• def_xref: PMID:17572666
• xref: Wikipedia:Retrosplenial_cortex

Fix this →

2. Typo still present: "retrospleninal" → "retrosplenial" (src/templates/hra-brain.template.tsv, line 5)

Same misspelling also remains in bulk_ntr_workflow/outputs/definitions/input/uberon_0002967.json and bulk_ntr_workflow/outputs/hra-brain-reports/input.tsv. Fix this →

3. Three terms still lack real literature references in def_xref — only ASCTB-TEMP placeholder IRIs:

Term	ID	Line
extended amygdala	UBERON_9920005	6
occipitoparietal transition region	UBERON_9920015	13
occipitotemporal transition region	UBERON_9920017	14

This fails QC checklist item 2 ("Every term has a real PMID/DOI — ASCTB-TEMP placeholder IRIs do not count").

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🟡 IMPORTANT

4. UBERON_9920004 overlap with existing UBERON:0013531 (retrosplenial region) still undocumented

candidates.tsv flags this as a possible_match — both cover Brodmann areas 26/29/30. Verified UBERON:0013531 is an active term (is_a: regional part of brain, part_of: cingulate cortex, synonym "retrosplenial cortex"). The gyrus-vs-cortex distinction (paralleling UBERON:0002756 anterior cingulate gyrus vs UBERON:0009835 anterior cingulate cortex) is reasonable, but as long as issue #1 (PENDING) is unresolved this can't be assessed in the actual template row, and no disambiguating xref/relationship to UBERON:0013531 has been added.

5. New reviewer feedback (RiveraAndrea83, 2026-06-15) raises additional scope concerns not yet addressed:

• Several of these terms are already present and better characterized in HOMBA (referencing https://alleninstitute.github.io/CCF-MAP/docs/HOMBA_ontology_v1.html) — worth checking for alignment/reuse rather than independent definitions.
• ifs1–ifs4 (the four inferior frontal sulcus subdivisions) are described as "not used" and the reviewer suggests excluding them at this stage.
• Some terms are transition zones between two regions with weak supporting evidence (consistent with issue 2 other dangling references #3 above — occipitoparietal/occipitotemporal transition region have no real citation).

This PR should not merge until a curator decides how to weigh this domain-expert feedback against the current term list — it may mean dropping ifs1–ifs4 and/or the two transition-region terms rather than sourcing new PMIDs for them.

6. ifj1/ifj2 remain unresolved — correctly excluded from the template, still flagged REQUIRES_CLARIFICATION_FROM_SOURCE in manual_curation.tsv. Should be tracked as a follow-up with ASCTB data providers, not a blocker.

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🔵 SUGGESTIONS

7. ifs1–ifs4 source labels not retained as synonyms — name_corrections.tsv recommends keeping them as exact_synonym for atlas-to-ontology mapping; the template has no synonym column populated. (Moot if issue #5 leads to dropping these terms instead.)

8. PR still has no description — a summary of what's added/excluded and the curatorial reasoning (especially for the retrosplenial gyrus/cortex distinction) would materially help review.

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Summary

Hierarchy/parents for the other 9 terms remain anatomically consistent and no obsolete terms are referenced. However, this PR is not mergeable as-is: the template still contains an unloadable [PENDING] row with a typo in the term name, three terms lack real literature support, and new domain-expert feedback suggests the term list itself (ifs1–4, transition regions) may need to shrink rather than just gain citations. Requesting changes again — the prior review's blocking items are unchanged since May 25.

[cellsemantic]

Reports relocated. Route: manual hand-edit (~12 terms, <20). TODO: per @RiveraAndrea83, drop ifs1-4 and weak transition-zone terms before adding; some terms are already well-characterised in HOMBA — check for duplicates first.

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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]

Re-review after the latest commit (877206a), which only relocated report artifacts out of src/templates/. All previously-flagged blocking issues remain unresolved:

CRITICAL:

1. UBERON_9920004 "cingulate gyrus, retrospleninal part" still has a [PENDING] definition and empty is_a/part_of — cannot be loaded by ROBOT. Resolution values already exist in bulk_ntr_workflow/outputs/definitions/uberon_0002967.json.
2. Typo "retrospleninal" → "retrosplenial" still present throughout.
3. extended amygdala, occipitoparietal transition region, and occipitotemporal transition region still have only ASCTB-TEMP placeholder IRIs as def_xref — no real PMID/DOI.

IMPORTANT:
4. Overlap between UBERON_9920004 and existing UBERON:0013531 (retrosplenial region) still undocumented — no disambiguating xref added.
5. New reviewer feedback (RiveraAndrea83) flags that several terms overlap with better-characterized HOMBA terms, that ifs1–ifs4 are "not used" and should likely be dropped at this stage, and that the transition-region terms lack solid supporting evidence — this needs curator resolution before merge, and may mean shrinking the term list rather than just sourcing citations.
6. ifj1/ifj2 correctly excluded but still need follow-up with ASCTB data providers.

Full details in the PR comment.

[ai4c-agent]

Claude finished @zhengj2007's task in 2m 38s —— View job

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PR Review: add hra brain terms (re-review, 3rd pass)

Review checklist:

• Hierarchy and parents are consistent (for the 9 fully-resolved terms)
• Definitions and supporting references look adequate
• Obsolete or replacement handling is safe
• OBO and ODK conventions appear preserved
• No obvious CI, auth, or workflow regression

---

What changed since the last review

Nothing. I confirmed via git diff 877206a..HEAD -- src/templates/hra-brain.template.tsv bulk_ntr_workflow/outputs/ that the only new commit (2ab42a8) is a merge from master with zero changes to the HRA brain content — the template, JSON, and report files are byte-for-byte identical to the state reviewed on 2026-07-09. All previously-flagged blocking items remain open.

🔴 CRITICAL (unresolved since 2026-05-25)

1. UBERON_9920004 still has [PENDING] definition and empty is_a/part_of (src/templates/hra-brain.template.tsv line 5) — ROBOT cannot load this row. The resolution already exists in bulk_ntr_workflow/outputs/definitions/uberon_0002967.json: definition text, is_a: UBERON:0000200 (gyrus, verified active), part_of: UBERON:0002967 (cingulate gyrus, verified active), def_xref: PMID:17572666. See inline comment.
2. Typo "retrospleninal" → "retrosplenial" — still present in the template label, bulk_ntr_workflow/outputs/definitions/input/uberon_0002967.json, and bulk_ntr_workflow/outputs/hra-brain-reports/input.tsv.
3. Three terms still lack real literature references, only ASCTB-TEMP placeholder IRIs as def_xref: extended amygdala (UBERON_9920005, line 6), occipitoparietal transition region (UBERON_9920015, line 13), occipitotemporal transition region (UBERON_9920017, line 14). See inline comments.

🟡 IMPORTANT

4. UBERON_9920004 overlap with UBERON:0013531 (retrosplenial region) is a real concern, not just hypothetical. I checked UBERON:0013531 directly in uberon-edit.obo: its definition already cites the same Brodmann areas 26/29/30, is_a: regional part of brain, part_of: cingulate cortex, with synonym "retrosplenial cortex". The gyrus-vs-cortex distinction proposed in candidates.tsv (paralleling UBERON:0002756 anterior cingulate gyrus vs UBERON:0009835 anterior cingulate cortex) is a reasonable pattern, but no disambiguating xref/relationship to UBERON:0013531 has been added, and this can't be properly assessed while the row is still [PENDING].
5. Domain-expert feedback from RiveraAndrea83 (2026-06-15) is still unaddressed: several terms may duplicate better-characterized HOMBA terms; ifs1–ifs4 are described as "not used" and suggested for exclusion; the two transition-region terms have weak supporting evidence (consistent with issue 2 other dangling references #3 — no real citations found for either). The maintainer thread (@cellsemantic, 2026-07-09) also records a TODO to drop ifs1-4 and weak transition-zone terms and check for HOMBA duplicates before merging — this has not yet been done in the template.
6. ifj1/ifj2 remain correctly excluded from the template but still need follow-up with ASCTB data providers (tracked in manual_curation.tsv as REQUIRES_CLARIFICATION_FROM_SOURCE) — not a blocker, just a reminder this is still open.

🔵 SUGGESTIONS

7. ifs1–ifs4 source labels not retained as exact_synonym (moot if these are dropped per issue "superficial cervical lymph node" term request #5).
8. PR still has no description explaining what was added/excluded and the curatorial reasoning.

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Summary

No progress has been made on this PR since the 2026-07-09 review — the only new commit is an empty merge from master. The template still contains an unloadable [PENDING] row with a name typo, three terms without real citations, and unresolved maintainer guidance (from @cellsemantic/@RiveraAndrea83) to drop ifs1–ifs4 and check for HOMBA duplicates before merging. Requesting changes again.

[ai4c-agent]

🔴 CRITICAL (unresolved since first review, 2026-05-25): This row still has [PENDING] as the definition and empty is_a/part_of columns for UBERON_9920004 "cingulate gyrus, retrospleninal part". ROBOT cannot load this row.

Also note the typo: "retrospleninal" → should be "retrosplenial" (also present in bulk_ntr_workflow/outputs/definitions/input/uberon_0002967.json and bulk_ntr_workflow/outputs/hra-brain-reports/input.tsv).

The resolved values already exist in bulk_ntr_workflow/outputs/definitions/uberon_0002967.json:

• Definition: "A subdivision of the cingulate gyrus located in its posterior-most region, corresponding to the retrosplenial cortical areas and comprising Brodmann areas 26, 29, and 30."
• is_a: UBERON:0000200 (gyrus) — verified active
• part_of: UBERON:0002967 (cingulate gyrus) — verified active
• def_xref: PMID:17572666

I additionally checked UBERON:0013531 ("retrosplenial region"): its existing definition already cites the same Brodmann areas 26/29/30 and is is_a: regional part of brain, part_of: cingulate cortex. This is a real overlap risk (flagged in candidates.tsv as possible_match), not just a hypothetical one — please add a disambiguating xref/relationship to UBERON:0013531 and document the gyrus-vs-cortex distinction (paralleling UBERON:0002756 vs UBERON:0009835) in the PR description before merge.

[ai4c-agent]

🔴 CRITICAL (unresolved): def_xref for "extended amygdala" (UBERON_9920005) is only the ASCTB-TEMP placeholder IRI — no real PMID/DOI, failing the workflow's own QC checklist ("Every term has a real PMID/DOI — ASCTB-TEMP placeholder IRIs do not count").

[ai4c-agent]

🔴 CRITICAL (unresolved): def_xref for "occipitoparietal transition region" (UBERON_9920015) is only the ASCTB-TEMP placeholder IRI, no real citation. Combined with 🟡 issue #5 below (reviewer RiveraAndrea83 flags this as a weakly-supported transition-zone term), consider whether this term should be dropped rather than sourced.

[ai4c-agent]

Re-review (3rd pass): the branch has had no substantive changes since the 2026-07-09 review — the only new commit is an empty merge from master. All previously-flagged CRITICAL and IMPORTANT issues remain unresolved:

CRITICAL:

1. UBERON_9920004 "cingulate gyrus, retrospleninal part" still has a [PENDING] definition and empty is_a/part_of — cannot be loaded by ROBOT. Resolution values already exist in bulk_ntr_workflow/outputs/definitions/uberon_0002967.json (verified is_a: UBERON:0000200 and part_of: UBERON:0002967 are both active terms).
2. Typo "retrospleninal" → "retrosplenial" still present throughout.
3. extended amygdala, occipitoparietal transition region, and occipitotemporal transition region still have only ASCTB-TEMP placeholder IRIs as def_xref — no real PMID/DOI.

IMPORTANT:
4. Overlap between UBERON_9920004 and existing UBERON:0013531 (retrosplenial region) is confirmed as a real concern (both cite Brodmann areas 26/29/30) and remains undocumented/undisambiguated.
5. Maintainer/domain-expert feedback (RiveraAndrea83, cellsemantic) to drop ifs1-4 and weak transition-zone terms and check for HOMBA duplicates has not been actioned in the template.
6. ifj1/ifj2 correctly excluded but still need ASCTB follow-up (non-blocking).

Full details in the PR comment and inline comments on src/templates/hra-brain.template.tsv.

[ai4c-agent]

Claude encountered an error after 1s —— View job

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I'll analyze this and get back to you.

[zhengj2007]

Removed the folder bulk_ntr_workflow/outputs/definitions, including all files within it.
Also removed the following files:

• src/templates/hra-brain-groups.template.tsv
• bulk_ntr_workflow/outputs/template_groups_initial.tsv
• bulk_ntr_workflow/outputs/template_initial.tsv

Updated src/templates/hra-brain.template.tsv

1. Remove the term “cingulate gyrus, retrosplenial part”, as it requires clarification from a domain expert.
2. Added def_xref values to the following three terms:

• extended amygdala — PMID:12724159
• occipitoparietal transition region — PMID:39976051
• occipitotemporal transition region — PMID:39976051

3. The ID range assigned to ORCID 0000-0002-2999-0103 is: xsd:integer[>= 8930000, < 8931000] Reassigned IDs to the new terms starting from UBERON:8930234.