Add HRA lymph NTR template (41 new terms)

[zhengj2007]

Generated via bulk_ntr_workflow from source_data/lymph.csv (46 input rows).

Pipeline completed through Stage 4:

• 41 new UBERON terms in leaf template
• 0 group terms
• 3 confirmed existing matches excluded
• 1 out-of-scope term excluded
• 1 manual-curation term flagged
• 7 name corrections reported

Resolved final pending row by removing
'ASCTB-TEMP_medial-lymph-node-of-common-illiac-lymph-nodes' from template, as it is a confirmed existing match to UBERON:0037532 (recorded in candidates.tsv).

[ai4c-agent]

Claude finished @zhengj2007's task in 6m 18s —— View job

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PR Review: Add HRA lymph NTR template (41 new terms)

• Gather context and understand the request
• Read template files and source data
• Review definitions and references
• Check parent term consistency in ontology
• Check OBO/ODK conventions
• Post final review summary

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Review Checklist

• Hierarchy and parents are consistent — FAIL (see critical issues distinguish between part_of and containment/located in #1, Disjoint_over undefined #2, peripheral lymph node #4 below)
• Definitions and supporting references look adequate — PARTIAL (many terms lack PMID support)
• Obsolete or replacement handling is safe — N/A (no obsoletions)
• OBO and ODK conventions appear preserved — FAIL (UNRESOLVABLE: prefixes, duplicate FMA xrefs)
• No obvious CI, auth, or workflow regression — PASS (no workflow files touched)

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🔴 CRITICAL Issues

1. UNRESOLVABLE: prefix in part_of fields — will break the ROBOT build

Six terms in src/templates/hra-lymph.template.tsv have invalid OBO IDs in the part_of column:

Term	Bad part_of value
UBERON_8930108 — anterior lymph trunk of accompanying suprarenal vein	UNRESOLVABLE:suprarenal vein region
UBERON_8930110 — collecting lymph trunk of lymphatics of soft parts covering posterior thoracic wall	UNRESOLVABLE:posterior thoracic wall
UBERON_8930123 — left lateral aortic lymph node	UNRESOLVABLE:left lateral aortic region
UBERON_8930135 — posterior extrathoracic lymph node	UNRESOLVABLE:posterior extrathoracic region
UBERON_8930141 — right lateral aortic lymph node	UNRESOLVABLE:right lateral aortic region
UBERON_8930144 — subclavicular lymph node	UNRESOLVABLE:subclavicular region

UNRESOLVABLE: is not a recognised OBO/ROBOT prefix. ROBOT will either fail to parse the template or produce malformed OWL axioms. These cells must be either left blank (no part_of) or replaced with valid UBERON IDs before the template can build.

2. Semantically wrong part_of — UBERON:0001631 is the thoracic duct, not an intercostal region

• hra-lymph.template.tsv row 9 (UBERON_8930115 — efferent lymphatics from fifth or sixth lowermost intercostal spaces): part_of UBERON:0001631
• Row 10 (UBERON_8930116 — efferent lymphatics from third, fourth, and fifth intercostal spaces): part_of UBERON:0001631

UBERON:0001631 = thoracic duct. The definitions correctly state these vessels drain toward the thoracic duct, but they are not part of the thoracic duct. There is no intercostal space term in UBERON, so the part_of should either be removed or pointed to a thoracic region (e.g. thoracic wall).

3. Duplicate FMA:12775 xref will corrupt cross-reference mappings

• UBERON:0035520 (anterior mediastinal lymph node) already has xref: FMA:12775 — this is the correct mapping.
• UBERON_8930121 (left anterior mediastinal lymph node) also gets xref: FMA:12775.
• UBERON_8930124 (lymph node of superior lymphatic collecting vessel of left lung) also gets xref: FMA:12775.

Three UBERON terms sharing one FMA ID will produce three-way bidirectional mapping conflicts. The two new terms should either have no FMA xref, or be mapped to distinct FMA IDs (if they exist).

4. "left lateral aortic lymph node" name collides with an existing RELATED synonym in UBERON:0016386

id: UBERON:0016386
name: paraaortic lymph node
synonym: "left lateral aortic lymph node" RELATED [FMA:16604]

The new term UBERON_8930123 uses exactly this string as its primary label. If a new separate concept is justified, the RELATED synonym on UBERON:0016386 must be updated or removed before merging to avoid label duplication. Similarly, the candidates.tsv marks this as only a possible_match, so the decision to create a new term warrants explicit curator sign-off.

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🟡 IMPORTANT Issues

5. "epitrochlear lymph node" (UBERON_8930117) may be redundant with UBERON:0038870

candidates.tsv notes UBERON:0038870 (cubital lymph node) as a possible match, with the recommendation that "epitrochlear should be added as a synonym to cubital lymph node, or if it represents a distinct structure that requires a new term." The workflow creates a new term without resolving this ambiguity. If epitrochlear ≡ cubital (same anatomical entity), a new term is wrong — epitrochlear should be added as a synonym to UBERON:0038870 instead.

6. part_of UBERON:0007302 is semantically imprecise for UBERON_8930113

• UBERON:0007302 = pectoral appendage vasculature (a vasculature, not an anatomical region)
• Used as part_of for "deep radial lymphatic channel", which the definition places specifically in the forearm

A lymphatic vessel is typically part_of an anatomical region (e.g. forelimb zeugopod UBERON:0002386). Making it part_of the entire vasculature of the pectoral appendage is both too broad and ontologically odd (vessels are not usually part_of a vasculature in this way).

7. part_of target too broad for UBERON_8930121

• "left anterior mediastinal lymph node" has part_of UBERON:0003728 (mediastinum — the entire central thoracic cavity)
• UBERON:0008820 (anterior mediastinum) is available and would be a more precise target consistent with the definition

8. part_of UBERON:0035520 is an unusual pattern for UBERON_8930124

• "lymph node of superior lymphatic collecting vessel of left lung" is specified as part_of UBERON:0035520 (anterior mediastinal lymph node)
• In UBERON, anatomical structures are typically part_of regions (spaces/organs), not part_of other lymph nodes. This needs anatomical verification.

9. ~15 terms lack PMID support

The following terms have only an ASCTB-TEMP URI as def_xref — no peer-reviewed literature:

• UBERON_8930108, 8930109, 8930110, 8930121, 8930125, 8930126, 8930130, 8930131, 8930133, 8930135, 8930138, 8930142, 8930143, 8930144, 8930151, 8930152

UBERON guidelines prefer at least one PMID per definition. The ASCTB-TEMP IRI is a provenance link to the HRA source, not a citable publication.

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🔵 Suggestions

10. "circumflex lymphatic channel" (UBERON_8930109) has no part_of and the definition does not name the specific anatomical structure it encircles — "around an anatomical structure" is uninformative. Consider specifying the structure or adding a narrower part_of.

11. "right lateral aortic lymph node" (UBERON_8930141): Unlike its left counterpart, UBERON:0016386 does not carry "right lateral aortic lymph node" as a synonym, so there is no pre-existing label conflict. The is_a parent (UBERON:0016386) is appropriate.

12. "left anterior mediastinal lymph node" (UBERON_8930121) part_of choice: Consider part_of UBERON:0008820 (anterior mediastinum) rather than part_of UBERON:0003728 (mediastinum) for consistency with the right-side analogue UBERON_8930139, which correctly uses part_of UBERON:0008820.

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Summary

This PR introduces a well-structured NTR template from the HRA lymph source data. The pipeline-level decisions (excluded confirmed matches, flagged manual curation items, corrected naming errors) are documented and largely sound. However, four critical issues must be resolved before the template can build and produce valid OWL:

1. Remove or replace the six UNRESOLVABLE: values in part_of cells.
2. Fix the two part_of UBERON:0001631 (thoracic duct) assignments for the intercostal efferent lymphatic terms.
3. Remove FMA:12775 xrefs from UBERON_8930121 and UBERON_8930124 (already used by UBERON:0035520).
4. Resolve the "left lateral aortic lymph node" label/synonym collision with UBERON:0016386.

Additionally, the epitrochlear/cubital overlap (issue #5) warrants explicit curator verification before the term is committed to the ontology.

[ai4c-agent]

Four critical issues must be resolved before this template can build:

1. UNRESOLVABLE: prefix in part_of fields for 6 terms — not a valid OBO/ROBOT IRI, will break the build.
2. Wrong part_of parent: UBERON_8930115 and UBERON_8930116 use part_of UBERON:0001631 (thoracic duct), but these vessels drain toward the thoracic duct — they are not part of it.
3. Duplicate FMA:12775 xref: UBERON_8930121 and UBERON_8930124 both carry FMA:12775, which is already mapped to UBERON:0035520. Three-way mapping conflict will corrupt cross-references.
4. Label collision: "left lateral aortic lymph node" (UBERON_8930123) duplicates an existing RELATED synonym on UBERON:0016386; the synonym on the existing term must be updated or removed.

Additional important items: epitrochlear lymph node (UBERON_8930117) possible redundancy with UBERON:0038870 needs curator sign-off; ~15 terms lack PMID support; several part_of targets need review (UBERON:0007302 for UBERON_8930113; UBERON:0003728 vs :0008820 for UBERON_8930121). Full details in the inline review comment.