Add HRA palatine-tonsil NTR template (7 new terms)

[zhengj2007]

Generated via bulk_ntr_workflow from source_data/palatine-tonsil.csv.

Pipeline completed through Stage 4:

• 7 new UBERON terms in leaf template
• 0 group terms
• 0 confirmed matches excluded
• 0 out-of-scope exclusions
• 0 manual-curation exclusions

Parent mapping handled in Stage 3 for mixed source parents:

• UBERON parents (4)
• ASCTB-TEMP parents (2)
• FMA parent mapping (1)

Final template has no [PENDING], INFER, NEEDS_MAPPING, or UNRESOLVABLE markers.

[ai4c-agent]

Claude finished @zhengj2007's task in 7m 29s —— View job

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PR Review: HRA Palatine-Tonsil NTR Template (7 new terms)

Review 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
• No obvious CI, auth, or workflow regression

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Review Summary

The 7 new terms are anatomically well-chosen and fill genuine gaps in the tonsil substructure representation. Parent-term resolution is mostly correct and consistent with analogous existing terms (the germinal center dark/light zones correctly follow the UBERON:8410052/UBERON:8410053 lymph-node precedent with is_a: UBERON:0001744). However, one critical build issue and one important structural omission need to be fixed before merge.

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🔴 CRITICAL — Templates not registered in src/ontology/uberon-odk.yaml

Stage 5 of the NTR workflow (registering templates with ODK) was not completed. Neither hra-palatine-tonsil.template.tsv nor hra-palatine-tonsil-groups.template.tsv appear in src/ontology/uberon-odk.yaml as component products. Without this registration, ROBOT will never process the templates and the 7 new UBERON terms (8930153–8930159) will not be built into any ontology artifact.

The pattern to add (following the existing hra_skeleton.owl precedent):

    - filename: hra_palatine_tonsil.owl
      use_template: true
      templates:
        - hra-palatine-tonsil.template.tsv
    - filename: hra_palatine_tonsil_groups.owl
      use_template: true
      templates:
        - hra-palatine-tonsil-groups.template.tsv

After editing the YAML, sh run.sh make update_repo (or the register_templates.py script from the workflow) must be run to regenerate the Makefile. Fix this →

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🟡 IMPORTANT — tonsil germinal center mantle zone (UBERON:8930157) missing part_of

The definition explicitly states "A part of the secondary follicle of the tonsil", yet the part_of column is empty in the template (src/templates/hra-palatine-tonsil.template.tsv, row 7). The term will be placed as is_a: UBERON:0010755 ! secondary follicle corona only, with no explicit tonsil localisation. An explicit part_of UBERON:8930158 (tonsil secondary follicle — added in the same template) should be added.

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🟡 IMPORTANT — tonsil follicle (UBERON:8930154) scope mismatch between name and definition

The definition reads "A lymphoid follicle that is part of a palatine tonsil" and part_of is UBERON:0002373 ! palatine tonsil, yet the label is tonsil follicle (not palatine tonsil follicle). Compare: tonsil germinal center (UBERON:0013688) uses the general part_of UBERON:0002372 ! tonsil. Either:

• Broaden the definition/part_of to the general tonsil (UBERON:0002372) to match the name, or
• Rename to palatine tonsil follicle to match the definition.

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🔵 SUGGESTION — tonsil T cell zone xref FMA:55221 may be imprecise

The input errors report flags FMA:55221 as "Diffuse lymphoid tissue" — a broad FMA concept used as the original parent mapping. Moving it to an xref rather than a parent is correct, but a generic "Diffuse lymphoid tissue" xref on a specifically-named T cell zone may mislead downstream users. If there is no more specific FMA term, consider removing this xref.

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Notes (no action required)

• ID range: UBERON:8930153–8930159 fall within [>= 8930000, < 8931000] allocated to Jie Zheng. ✓
• is_a: UBERON:0001744 for dark/light zones: consistent with existing UBERON:8410052/8410053. ✓
• ASCTB-TEMP IRIs in def_xref: standard HRA provenance pattern with real PMIDs also present. ✓
• present_in_taxon: NCBITaxon:9606: appropriate for HRA terms. ✓
• PMIDs 25656706 and 8011279 verified in existing UBERON terms. PMIDs 34430822, 417886, 11789984, 28844822, 30801022 should be manually verified for relevance.
• Empty groups template (headers only) is correct — all 7 terms are leaf terms. ✓

[ai4c-agent]

Two issues need fixing before merge:

1. 🔴 CRITICAL — Templates not registered in uberon-odk.yaml: Stage 5 of the NTR workflow was not completed. Neither hra-palatine-tonsil.template.tsv nor hra-palatine-tonsil-groups.template.tsv appear as component products in src/ontology/uberon-odk.yaml. Without this, ROBOT will not process the templates and the 7 new terms (UBERON:8930153–8930159) will not be built into any ontology artifact. Add entries following the hra_skeleton.owl pattern and regenerate the Makefile.

2. 🟡 IMPORTANT — tonsil germinal center mantle zone (UBERON:8930157) missing part_of: Definition says 'A part of the secondary follicle of the tonsil' but the part_of column is empty. Should have part_of UBERON:8930158 ! tonsil secondary follicle.

Also: tonsil follicle (UBERON:8930154) label vs definition scope mismatch (name implies general tonsil scope but definition/part_of is palatine-tonsil-specific).

Full review details in the Claude comment above.