Add HRA spleen NTR batch outputs and review reports

[zhengj2007]

Generated via bulk_ntr_workflow from source_data/spleen.csv.

Pipeline completed through Stage 4:

• 9 new UBERON leaf terms in final template
• 0 group terms
• 1 confirmed existing match excluded
• 0 possible matches identified
• 0 out-of-scope terms
• 0 manual-curation items

QC status:

• 0 [PENDING] definitions
• 0 INFER/UNRESOLVABLE/NEEDS_MAPPING markers

Includes:

• Template and groups TSVs in src/templates/
• Detailed review reports: candidates, errors, input, name_corrections
• Source data snapshot in bulk_ntr_workflow/source_data/

Signed-off-by: @dragon-ai-agent

[ai4c-agent]

Claude finished @zhengj2007's task in 5m 5s —— View job

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PR Review: Add HRA spleen NTR batch outputs and review reports

Checklist:

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

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Summary

This PR adds ROBOT template outputs for 9 new spleen anatomy terms (IDs UBERON:8930191–UBERON:8930199), allocated to Jie Zheng in idranges.owl (idrange:42). Pipeline stages 1–4 completed cleanly: 0 errors, 0 pending definitions, 1 confirmed existing match excluded (Connective tissue → UBERON:0002384). References are generally well-supported with multiple DOIs/PMIDs.

Several issues need attention before merge or before the template is applied via ROBOT:

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🟡 IMPORTANT Issues

1. Malformed DOI URL in arterial capillary def_xref

src/templates/hra-spleen.template.tsv, line 3 — the first DOI contains spaces:

https://doi.org/ 10.1182/ bloodadvances.2017015073

This URL is invalid and will produce a malformed xref in the ontology. Correct form: https://doi.org/10.1182/bloodadvances.2017015073 (also duplicated correctly later in the same cell as DOI:10.1182/bloodadvances.2017015073). The malformed version originates from the source data (spleen.csv line 3) and carried through unchanged.
Fix this →

2. Space in PMID reference for Superficial Mantle Zone

src/templates/hra-spleen.template.tsv, line 10 — def_xref contains PMID: 20126587 (space after colon). This should be PMID:20126587 with no space per standard OBO xref formatting.

3. Non-standard capitalisation in LABEL values

UBERON convention uses lowercase for anatomical term names (compare periarterial lymphatic sheath, splenic sinusoid, white pulp of spleen). The following labels violate this:

Current label	Suggested label
Inner Mantle Zone	inner mantle zone
Superficial Mantle Zone	superficial mantle zone
Ring Fiber	ring fiber
Splenic Red Pulp Stroma	splenic red pulp stroma
Inner PALS	inner periarterial lymphatic sheath
Outer PALS	outer periarterial lymphatic sheath

The pipeline's name_corrections.tsv caught three labels (Arterial Capillary, White Pulp Lymphatic Vessels, Subcapsule) but missed these five. The original capitalised forms should be added as synonyms.

4. "Inner PALS" / "Outer PALS" — abbreviation should be expanded

"PALS" stands for periarterial lymphatic sheath (= UBERON:0001960). Using an abbreviation as the primary label is not UBERON convention. The labels should be inner periarterial lymphatic sheath and outer periarterial lymphatic sheath, with PALS retained as a synonym.

5. Ring Fiber is_a UBERON:0006804 (reticular tissue) — potential classification error

UBERON:0006804 is defined as a type of tissue (reticular connective tissue). A ring fiber is an individual structural fiber, not a tissue type. Classifying ring fiber is_a reticular tissue is logically imprecise — a ring fiber is a component of reticular tissue, not a subtype of it. UBERON does not appear to have a dedicated "reticular fiber" class, so this may require either:

• Using UBERON:0000061 (anatomical structure) as a fallback is_a, with part_of UBERON:0003910 (splenic sinusoid) preserved, or
• Curator review to identify a more appropriate structural parent.

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🔵 Suggestions

6. arterial capillary — no part_of relationship

The term is defined in general terms (not spleen-specific), with only is_a capillary. If this is intentionally a general capillary subtype term, that is fine, but the definition's example context of the spleen is not captured in any relationship. Consider noting in the definition or adding a Present_in_taxon annotation that this applies to mammalian vasculature generally. (If the term is meant to be spleen-specific it should have a part_of red pulp of spleen relationship.)

7. Stage 5 (ODK registration) is pending

The templates are staged in src/templates/ but have not yet been registered in src/ontology/uberon-odk.yaml. This must happen before the ROBOT build can use them. Consider whether this should be part of this PR or a follow-up.

8. ASCTB-TEMP IRIs in def_xref

All terms include https://purl.org/ccf/ASCTB-TEMP_* URIs in the def_xref column. Per the workflow's own QC checklist, these do not count as bibliographic references. They are acceptable as cross-references but should be moved to the xref column rather than def_xref to keep the definition citation column clean.

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Parent term verification

All UBERON parent IDs resolve correctly:

Term	is_a	part_of
arterial capillary	UBERON:0001982 capillary ✓	—
Inner/Superficial Mantle Zone	UBERON:0001744 lymphoid tissue ✓	UBERON:0010421 spleen B cell corona ✓
Inner/Outer PALS	UBERON:0000064 organ part ✓	UBERON:0001960 periarterial lymphatic sheath ✓
Ring Fiber	UBERON:0006804 reticular tissue ⚠️	UBERON:0003910 splenic sinusoid ✓
Splenic Red Pulp Stroma	UBERON:0003891 stroma ✓	UBERON:0001250 red pulp of spleen ✓
subcapsular zone	UBERON:0000064 organ part ✓	UBERON:0002106 spleen ✓
white pulp lymphatic vessel	UBERON:0001473 lymphatic vessel ✓	UBERON:0001959 white pulp of spleen ✓

Recommendation: REQUEST CHANGES — The malformed DOI URL (issue 1), capitalization issues (issues 3–4), and the potential is_a misclassification for Ring Fiber (issue 5) should be resolved before this template is used to generate ontology terms.

[ai4c-agent]

Several issues need attention before this template is applied:

🟡 IMPORTANT:

1. Malformed DOI URL in 'arterial capillary' def_xref: 'https://doi.org/ 10.1182/ bloodadvances.2017015073' has spaces and is invalid.
2. 'PMID: 20126587' has a space after the colon in Superficial Mantle Zone def_xref.
3. Multiple LABEL values use non-UBERON capitalization: 'Inner Mantle Zone', 'Superficial Mantle Zone', 'Ring Fiber', 'Splenic Red Pulp Stroma', 'Inner PALS', 'Outer PALS' — all should be lowercase.
4. 'Inner PALS'/'Outer PALS' use an abbreviation; labels should be expanded to 'inner periarterial lymphatic sheath' / 'outer periarterial lymphatic sheath'.
5. Ring Fiber is_a UBERON:0006804 (reticular tissue): a ring fiber is an individual fiber, not a tissue type — this is_a parent may be a logical misclassification.

See the full review in the PR comment for details and suggestions.