Add HRA skeleton component with 386 new skeletal terms#3679
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RiveraAndrea83 merged 5 commits intomasterfrom Mar 25, 2026
Merged
Add HRA skeleton component with 386 new skeletal terms#3679RiveraAndrea83 merged 5 commits intomasterfrom
RiveraAndrea83 merged 5 commits intomasterfrom
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Integrate 386 new skeletal anatomical terms from HubMAP/HRA as an ODK template-based component (hra_skeleton.owl). Terms cover bone zones, projections, fossae, foramina and other skeletal features of the human skeleton, each with definitions, part_of axioms, xrefs, and present_in_taxon NCBITaxon:9606. Key changes: - Add src/templates/hra-skeleton.template.tsv (ROBOT template, 386 terms) - Add src/templates/hra-skeleton-prefixes.owl (property declarations) - Configure component in uberon-odk.yaml and override build rule in uberon.Makefile to supply dcterms/dc prefix declarations - IDs assigned in automation range: UBERON:1200004–UBERON:1200389 - 4 problematic terms dropped (see corrections_report.md section 4) - Run update_repo to regenerate Makefile, catalog, and docs @dragon-ai-agent Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Removed terms whose labels exactly match existing UBERON exact synonyms: - 'cribiform plate of ethmoid bone' (duplicate of UBERON:0004546 cribriform plate) - 'styloid process of petrous part of temporal bone' (duplicate of UBERON:0003960) 384 terms remain. IDs re-assigned contiguously: UBERON:1200004–UBERON:1200387. ~100 additional "feature of bone" terms may overlap with existing generic feature terms (e.g. 'acetabular fossa of os coxa' vs UBERON:0014445 'acetabular fossa') — these require curator review to determine whether they are true duplicates or distinct bone-specific substructures. @dragon-ai-agent Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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Converted to draft for now as further local checks have detected likely duplicates. |
Removed 48 terms that duplicate existing UBERON terms: - Group A (16): same genus and part_of bone as existing term - Group B (32): same structure but existing term lacks part_of axiom 336 terms remain (UBERON:1200004–UBERON:1200339). 52 Group C candidates (different part_of granularity) are retained pending curator review. Reports added to src/templates/hra-skeleton-reports/: - duplicate_candidates_report.md: full analysis with untruncated definitions for all 100 candidates across Groups A, B, C - term_mapping_table.md: concise mapping of removed/retained terms to existing UBERON terms with brief explanations - corrections_report.md: moved from repo root @dragon-ai-agent Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
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#gogoeditdiff |
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@RiveraAndrea83 - I have removed the last batch of entries that likely map to existing Uberon terms. Good to merge if all tests pass. |
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#gogoeditdiff |
RiveraAndrea83
approved these changes
Mar 25, 2026
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Integrate 386 new skeletal anatomical terms from HubMAP/HRA as an ODK template-based component (hra_skeleton.owl). Terms cover bone zones, projections, fossae, foramina and other skeletal features of the human skeleton, each with definitions, part_of axioms, xrefs, and present_in_taxon NCBITaxon:9606.
Key changes:
@dragon-ai-agent
Fixes #3678