Add hra muscular ntr#3700
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10 input terms processed by the new dual-template flow: - Stage 1: pre-classified into 8 leaf + 2 group rows - Stage 2: 8 group JSONs (7 leaf parent groups + 1 grouping_terms bucket) - Stage 3: 8 ntr-term-researcher agents (3 needed retry due to API stream timeouts; grouping_terms handled inline after retry stalled) - Stage 4: dual-template merge Final output: - 4 NEW leaf terms with Aristotelian definitions, real PMID/DOI refs, resolved is_a/part_of, Wikipedia + FMA xrefs - 0 NEW group terms — both 'anterior vertebral muscle' and 'circular pharyngeal muscle' resolved to existing UBERON terms via Step 2 OLS4 check, validating that confirmed_match takes precedence over Step 8 EC pattern detection - 5 confirmed_match (5 of 10 input terms already exist in UBERON): - ceratoglossus → UBERON:0008428 - chondroglossus muscle → UBERON:0011535 - costal diaphragm → UBERON:0035831 - aryepiglotticus muscle → UBERON:0011025 - constrictor muscle of pharynx → UBERON:0001569 (NEW from group flow) - 1 possible_match: anterior vertebral muscle ≈ UBERON:0008549 (prevertebral muscle) — flagged for curator decision (synonym vs new term) - 1 manual_curation: anterior vertebral muscle — UBERON's similar term uses attaches_to + innervated_by axioms, not the simple genus + part_of pattern, so out of EC template scope The test exercises: leaf+INFER parent, leaf+NEEDS_MAPPING:FMA parent, leaf+UNRESOLVABLE parent (including wrong-domain), group→confirmed_match, group→possible_match+manual_curation. All paths working as designed. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Claude finished @dosumis's task in 5m 44s —— View job PR Review: Add HRA Muscular NTRReview checklist:
SummaryThis PR adds ROBOT template infrastructure and four new NTR (New Term Request) leaf terms for HRA (Human Reference Atlas) muscular-system structures, along with a bulk NTR workflow toolkit. The term-level research appears careful and the definition quality is high. However, there are two issues that should be addressed before merge, and several important follow-on items. 🔴 CRITICAL1. New templates not registered in ODK config — they will never compile
The precedent is 2. The definition research output (
and sets 🟡 IMPORTANT3. Row 5 of 4. ASCTB-TEMP IRIs in the All four terms carry For example, The ASCTB-TEMP IRI is the third token in the definition xref list. 5. Missing Per 6.
🔵 SUGGESTIONS7. Binary Excel file in repo root
8. ISBN references are non-standard in OBO/UBERON; 9. FMA parent for articularis genu (UBERON:0004252) is very broad FMA:22424 "Muscle of anterior compartment of thigh" has no UBERON equivalent, so the workflow fell back to UBERON:0004252 "hindlimb stylopod muscle". The fallback is documented in the definition output and the errors report, but UBERON:0004252 is a very coarse grouping. The definition output itself suggests considering UBERON:0001377 (quadriceps femoris) and explicitly notes that "articularis genu is anatomically discrete from the quadriceps". Curator should confirm the fallback is acceptable or note it for a follow-up parent term request. 10. Using 11. The PR adds 1,700+ lines of Python scripts, JSON outputs, and documentation for the bulk NTR pipeline. This infrastructure is valuable but may belong in a separate utilities repository or be Per-term verdict
Confirmed matches correctly excluded from template: The term research quality and definition writing are solid. The main blockers are the missing ODK registration (templates won't compile without it) and the relationship-type inconsistency on UBERON:9900010. Addressing the missing |
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Two blocking issues before merge:
-
Templates not wired into the build —
hra-muscular.template.tsvandhra-muscular-groups.template.tsvare not registered inuberon-odk.yamloruberon.Makefile. Without equivalent entries to thehra-skeletonprecedent these terms will never compile into the ontology. -
Relationship-type conflict on UBERON:9900010 — the definition workflow output (
unresolvable_meningohypophyseal_artery.json) explicitly recommendspart_offordorsal part of intertransversarii laterales lumborum musclebut the template usesis_a. These need to be reconciled.
Also flagged as important (see full comment):
- UBERON:9900008 (clavicular head) has no
is_a, onlypart_of - ASCTB-TEMP IRIs in the
def_xrefcolumn should be inxref term_tracker_itemmissing from both templates- Report files under
src/templates/hra-muscular-reports/should not live inside the template directory
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Two blocking issues before merge:
-
Templates not wired into the build — hra-muscular.template.tsv and hra-muscular-groups.template.tsv are not registered in uberon-odk.yaml or uberon.Makefile. Without equivalent entries to the hra-skeleton precedent these terms will never compile into the ontology.
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Relationship-type conflict on UBERON:9900010 — the definition workflow output (unresolvable_meningohypophyseal_artery.json) explicitly recommends part_of for dorsal part of intertransversarii laterales lumborum muscle but the template uses is_a. These need to be reconciled.
Also flagged as important (see full comment):
- UBERON:9900008 (clavicular head) has no is_a, only part_of
- ASCTB-TEMP IRIs in the def_xref column should be in xref
- term_tracker_item missing from both templates
- Report files under src/templates/hra-muscular-reports/ should not live inside the template directory
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Two blocking issues before merge. 1) Templates not wired into the build: hra-muscular.template.tsv and hra-muscular-groups.template.tsv are not registered in uberon-odk.yaml or uberon.Makefile. 2) Relationship-type conflict on UBERON:9900010: workflow output says part_of but template uses is_a. See full review comment for details.
…umn assignment
Previously the agent picked is_a OR part_of and put the resolved parent in one
column, leaving the other empty. UBERON convention for specific named structures
is to populate BOTH — e.g. vastus lateralis (UBERON:0001379) has
'is_a UBERON:0001630 (muscle organ)' AND 'relationship: part_of UBERON:0001377
(quadriceps femoris)'.
ntr-term-researcher.md changes:
- Step 7 rewritten: agent now uses awk over uberon-edit.obo to find similar
specific UBERON terms, identifies the genus class (typically muscle organ
UBERON:0001630, muscle head UBERON:0011906) AND the part_of containing
structure, then populates leaf_template_rows[label] = {is_a, part_of}
- Worked examples included (clavicular head, articularis genu, dominant
follicle subtypes)
- Explicit warning: do NOT just take the source parent and assign it to one
column; the source parent is often too broad to serve as the genus
- Output JSON gains leaf_template_rows key (analogous to group_template_rows)
- Quality checks updated: prefer leaf_template_rows; both is_a and part_of
should be populated when applicable
merge_definitions.py changes:
- load_subagent_outputs reads leaf_template_rows
- merge_leaf_template uses leaf_template_rows first; falls back to legacy
resolved_relationships + resolved_parents if absent (backward compatible)
- New counter 'leaf_template_rows used' in summary output
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…lated After updating Step 7 of the agent spec to require obo-grep lookup of similar UBERON terms before assigning the parent, re-ran the 4 leaf-term agents on the muscular-system test set. All 4 now populate both is_a and part_of columns: | Term | is_a | part_of | |-----------------------------------------------------|--------------------|-------------------| | anterior cervical intertransversarii muscle | muscle organ | neck | | articularis genu muscle | muscle organ | hindlimb stylopod | | clavicular head of pectoralis major muscle | muscle head | pectoralis major | | dorsal part of intertransversarii laterales lumborum| muscle organ | lower back muscle | Notable: clavicular head correctly resolved to is_a UBERON:0011906 (muscle head) — matching the long head of biceps brachii (UBERON:0007168) precedent. articularis genu correctly distinguished UBERON:0004252 (sibling grouping class, not container) from UBERON:0000376 (the actual containing region) by following the pectineus precedent. Stage 4 reports leaf_template_rows used=4, legacy resolved_relationships=0 — confirms the new path is exercising the proper genus+location lookup rather than the legacy single-column assignment. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Standalone experiment in bulk_ntr_workflow/experiments/. Workflow scripts NOT modified. Tests whether an agent can extract origin/insertion/ innervation/action from Wikipedia + uberon-edit.obo with UBERON ID resolution and verbatim evidence quotes per field. Test set (well-known whole muscle → obscure sub-part): - internal abdominal oblique muscle (existing UBERON:0005454) - tensor fascia latae muscle (existing UBERON:0001376) - iliocostalis cervicalis muscle (existing UBERON:0008546) - articularis genu muscle (NEW) - clavicular head of pectoralis major muscle (NEW, muscle head) - dorsal part of intertransversarii laterales lumborum (NEW, obscure) Findings (full report in SUMMARY.md): 1. All 6 terms got 5-6 of 6 enrichment fields populated. Where UBERON IDs couldn't be resolved (named attachments, specific nerves, specific bone landmarks), the agent gracefully fell back to free-text quotes plus parent-class UBERON IDs. 2. The hypothesis that 'muscle parts are poorly axiomatised' is partly confirmed: parent muscle classes for sub-parts are missing (intertransversarii laterales lumborum), but the bigger gap is in UBERON's coverage of related anatomical entities — superior gluteal nerve, lateral pectoral nerve, iliotibial tract, suprapatellar bursa, ilioinguinal nerve, linea alba, accessory process of lumbar vertebra are all missing. A famous muscle like tensor fasciae latae has 2 such gaps; the obscure dorsal sub-part has 3 — gaps are not strongly correlated with term obscurity. 3. The verbatim-quote design works well for review. Each enrichment field carries 1-3 sentences of evidence + a source URL, making the enrichment auditable in seconds per field. 4. 3 of 6 picks turned out to be already in UBERON despite being plausible NTR candidates — Step 2 (existing-term check) continues to do real work. Existing UBERON stanzas often have surprisingly light axiomatisation (tensor fasciae latae has only 1 origin axiom), so enrichment could also improve existing terms, not just new ones. No workflow changes; results are reference material for a future enrichment phase. Roadmap candidates: (a) system-specific templates with pre-extracted fields per system, (b) standardised evidence-quote design across all fields, (c) cascade detection — flag missing UBERON entities as candidate NTRs. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
User hypothesis: simple is_a + part_of would be sufficient for ovary terms (unlike muscles where origin/insertion/innervation are needed). Result: hypothesis NOT confirmed. 5 of 6 ovary terms tested require relations beyond is_a + part_of: - Layers (corona radiata, CL granulosa lutein, CL theca): need composed_primarily_of (CL:cell type) and/or bounding_layer_of, has_part - Compositional complex (cumulus oophorus oocyte complex): needs has_part to distinguish from cumulus oophorus alone - Follicle stages (early antral, transitional primary): need develops_from PLUS has_component with cardinality constraints PLUS has_potential_to_develop_into — UBERON's existing precedent (UBERON:0000035/36/37) uses all of these Why ovary is harder for simple is_a + part_of than expected: - Sibling layers share part_of (both lutein + theca layers part_of corpus luteum) — part_of alone doesn't differentiate - Sibling follicle stages share is_a (all primary/secondary/tertiary is_a ovarian follicle AND part_of ovary) — neither relation distinguishes - The defining property is cellular composition or developmental position, neither captured by spatial part_of Cross-experiment comparison: - Muscle group: simple genus + part_of EC sufficient (74% precedent) - Muscle individual: needs muscle origin/insertion/innervation - Muscle head/sub-part: simple is_a + part_of works (sparse precedent) - Ovary layer/complex/stage: needs composed_primarily_of, has_part, develops_from, cardinality Conclusion: per-system templates are warranted. A single one-size-fits-all leaf template either over-fits one domain or under-serves both. The evidence-quote JSON design transferred cleanly between domains — confirming it as a generalisable pattern. Output: bulk_ntr_workflow/experiments/SUMMARY_OVARY.md and 6 enriched JSONs. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Stage 1 now partitions input rows by source `tables` value into system overlays. Each overlay produces its own clean leaf template with system-specific columns; unmapped tables go to the default template. Phase 6 — develops_from on default leaf template - New optional column with directive `SC RO:0002202 some %` - Empty cell → no axiom (standard ROBOT pattern; do NOT alter directive to work around empty cells) - Populated by agent for stage series (follicle stages, embryonic stages, etc.) Phase 7 — skeletal-muscle overlay - New muscle template variant: <name>-muscle.template.tsv - Adds has_muscle_origin (RO:0002372), has_muscle_insertion (RO:0002373), innervated_by (RO:0002005) - All optional; populated by agent only with evidence-quoted UBERON IDs - Triggered by source table value `muscular-system` (SYSTEM_OVERLAYS map) Implementation notes: - generate_template.py: SYSTEM_OVERLAYS, classify_system(), overlay_paths(); per-row routing builds leaf_rows_by_overlay dict; one template TSV written per overlay - group_terms_by_parent.py: reads ALL leaf templates (default + system overlays) via discover_leaf_templates(); each per-term JSON entry now carries `system` field - merge_definitions.py: REFACTORED to use header-name lookup (header_indices()) instead of hardcoded column indices. Each leaf template variant's columns are looked up at merge time. Optional logic columns (develops_from, has_muscle_*) populate from leaf_template_rows[label] when both column and value exist. - agent spec: documents system field, develops_from + muscle-overlay guidance; output JSON example shows the optional fields - CLAUDE.md: column reference splits leaf table into default + muscle overlay; new partitioning subsection Smoke-tested with --table muscular-system --limit 10: - Step 0 routing correctly outputs muscle=8, group=2 (no default partition since all 10 rows are muscular-system) - Output template has 16 columns with the 6 expected logic relations (is_a + part_of + develops_from + 3 muscle) - Merge with existing leaf_template_rows from previous run still works via legacy is_a + part_of fallback (Optional cols filled: 0 because agents haven't been re-run with new spec) Phase 8 (term promotion) and overlays for skeleton/vasculature/nervous documented in ROADMAP only — not implemented. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Re-ran Stage 1 with --table muscular-system --limit 10. Output: - Step 0 routing: muscle=8, group=2 (correctly partitioned by source table) - <name>-muscle.template.tsv has 16 columns: 6 logic relations (is_a, part_of, develops_from, has_muscle_origin, has_muscle_insertion, innervated_by) + 10 metadata - Default leaf template absent (no rows for it — all are muscular-system) Re-ran one agent (articularis genu) with the updated spec. Agent emitted leaf_template_rows with the new optional muscle-overlay fields: is_a=UBERON:0001630 (muscle organ), part_of=UBERON:0000376 (thigh), has_muscle_origin=UBERON:0000981 (femur), innervated_by=UBERON:0001267 (femoral nerve). has_muscle_insertion correctly omitted (suprapatellar bursa not in UBERON). Merge correctly populated all 4 columns from leaf_template_rows (Optional cols filled: 2 in summary). The other 3 leaf JSONs were generated under the older agent spec — they fall back to legacy resolved_relationships and only get is_a OR part_of. To populate their muscle-overlay fields, those agents would need to be re-run. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Stage 1 partitioning: muscle=55, group=20 (no default partition)
Stage 2 grouping: 45 groups (44 leaf + 1 grouping_terms bucket of 20 group terms)
Stage 3: 45 agents in 6 parallel batches; all completed without API timeouts
Stage 4 merge results:
Leaf template <name>-muscle.template.tsv (25 new terms):
- Phase 7 muscle overlay populated: 68 optional column values across 25 rows
(avg 2.7 muscle-specific columns per term — origin/insertion/innervated_by)
- All 25 use leaf_template_rows (no legacy fallback path triggered)
- 0 PENDING definitions, 0 INFER relationships, 0 unresolved
- 24 of 25 have real PMID/DOI/ISBN def_xrefs added
Groups template <name>-groups.template.tsv (8 new terms):
- All 8 fit the simple genus + part_of some Y EC pattern
- Genus is UBERON:0014892 (skeletal muscle organ, vertebrate) for all 8
- Locations: thoracic cavity, sole of pes, dorsum, external/middle ear, etc.
Reports:
- candidates.tsv: 39 confirmed_matches (existing UBERON terms)
Notable: 9 of 20 grouping_terms already existed (prevertebral muscle,
constrictor muscle of pharynx, scalene, hypothenar, palmar/plantar
interosseous, splenius, facial muscle, intra-ocular muscle)
- manual_curation.tsv: 3 group terms not fitting simple part_of pattern
(pelvic floor, dorsum of foot, longitudinal pharyngeal — all need
new region/orientation terms OR has_part/membership-based modelling)
- name_corrections.tsv: 17 entries (typos like 'capitus' → 'capitis',
Latin variants like 'fascia' → 'fasciae', 'tibalis' → 'tibialis')
Wrong-domain parent issues flagged by agents (data quality in HRA source):
- sternum→diaphragm (costal/sternal parts)
- splenic artery→intrinsic muscle of tongue (inferior longitudinal)
- innominate bone→pharyngeal muscle (pterygopharyngeus)
- tip of renal papilla→hand muscle (palmar interosseous)
- meningohypophyseal artery→lumbar back muscle (dorsal intertransversarii)
- and many more — captured in individual JSON unresolvable notes
NOT merged to main. Branch retains everything for review.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Claude finished @dosumis's task in 5m 44s —— View job PR Review: Add HRA Muscular NTR (Re-review after sync)Review checklist:
Tasks:
SummaryThe PR has grown substantially since the first review: the original four-term ✅ Fixed since previous review
🔴 CRITICAL1. Templates still not registered in ODK config or Makefile Neither In - filename: hra_muscular.owl
templates:
- hra-muscular-muscle.template.tsv
- hra-muscular-groups.template.tsvAnd a corresponding build rule in 2. Groups template: three back-muscle terms have identical EC axiom definitions — reasoner will infer equivalence
The OWL reasoner will immediately conclude all three are equivalent classes. Grouping terms like these are usually defined via 🟡 IMPORTANT3. ASCTB-TEMP IRIs still in the All 33 terms still carry 4. Per 5. Pipeline outputs ( 6. Three leaf terms use
All other skeletal muscle leaf terms in the same template correctly use 7. UBERON:9900025 (lateral compartment of leg muscle) — The definition explicitly states the structure is "part of the lateral (fibular) fascial compartment of the leg". The 🔵 SUGGESTIONS8. ISBN citations are not standard OBO/UBERON practice. The TA2 URL ( 9. UBERON:9900047 (posterior abdominal wall muscle) — location is generic abdominal wall The EC axiom uses Per-template verdictLeaf template (25 terms) — most terms look anatomically sound with good definitions and PMIDs. Specific concerns:
Groups template (8 terms) — logical-definition structure is sound in principle, but three back-layer groupings share identical EC axioms (see critical issue 2 above). The remaining five groupings (ear, abdominal wall, sole, thoracic wall) each have unique location values and are fine. Two prior blockers are resolved. The remaining critical items (build registration and EC axiom collision) must be addressed before merge. |
This PR modifies some logical definitions. See details below:Number of classes with modified logical definitions: 5 http://purl.obolibrary.org/obo/UBERON_1100029No changes in inferred subclasses. http://purl.obolibrary.org/obo/UBERON_1100017Added subclasses: 3 http://purl.obolibrary.org/obo/UBERON_1100005No changes in inferred subclasses. http://purl.obolibrary.org/obo/UBERON_1100024Added subclasses: 1 http://purl.obolibrary.org/obo/UBERON_1100021Added subclasses: 4 |
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Two new critical issues must be fixed before merge:
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Templates still not registered in ODK config/Makefile — both hra-muscular-muscle.template.tsv and hra-muscular-groups.template.tsv are absent from uberon-odk.yaml and uberon.Makefile. No component build rule exists, so all 33 new terms will never compile.
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Groups template EC axiom collision — intermediate back muscle (UBERON:9900020), segmental back muscle (UBERON:9900055), and superficial back muscle (UBERON:9900063) all produce identical EquivalentClass axioms (skeletal muscle organ AND part_of dorsum). The reasoner will infer these three terms are equivalent. These grouping terms should use SC (SubClassOf) columns, not EC (EquivalentClass).
Fixed from prior review: UBERON:9900008 now has is_a (muscle head) ✅; UBERON:9900010 relationship conflict resolved ✅.
Still outstanding from prior review (IMPORTANT): ASCTB-TEMP IRIs remain in the def_xref column; term_tracker_item columns missing from both templates; hra-muscular-reports/ still under src/templates/.
See the full review comment for details and per-term verdict.
…m run 26 unresolvable notes extracted from per-term JSON outputs in bulk_ntr_workflow/outputs/definitions/. Most are wrong-domain parent issues in HRA source data (sternum→diaphragm, splenic artery→tongue muscle, innominate bone→pharyngeal muscle, meningohypophyseal artery→ lumbar muscle, anterior cerebral artery→hand muscle, fused sacrum→ abdominal muscle, etc.). Workflow gap noted: merge_definitions.py currently writes aggregated reports for confirmed_matches, name_corrections, out_of_scope, and manual_curation, but NOT for unresolvable. Adding this aggregation to the merge script would surface these systematically without manual extraction. Tracked for follow-up. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Replaces standalone unresolvable.tsv with a single curator-facing review file. Each row of the original input gets: | Column | Purpose | |-------------------------|-----------------------------------------------| | table, as_iri, label | Input source identifiers | | term_type | leaf | group | | source_parent_id | Parent ID from source data | | source_parent_label | Parent label from source | | status | confirmed_match | new_term_leaf | | | | new_term_group | manual_curation | | mapped_uberon_id | Either existing UBERON ID (if confirmed) | | | OR new UBERON:99xxxxx ID (if new term) | | label_correction | Suggested corrected label (typos etc.) | | label_correction_reason | Why the label was corrected | | parent_correction | Corrected parent UBERON ID (when source was | | | wrong-domain or missing) | | curator_notes | Pipe-separated unresolvable notes from agents | | | (wrong-domain parents, missing UBERON | | | entities, modelling caveats) | Aggregated stats for the muscular-system run: - 75 input rows - Status: 39 confirmed_match, 25 new_term_leaf, 8 new_term_group, 3 manual_curation - 17 with label corrections - 34 with parent corrections (parent_correction populated) - 20 with curator notes (mostly wrong-domain source parents) This is the file curators should review first — one row per input term, all findings consolidated, no need to dig into per-term JSONs. Built one-off via Python script joining input.tsv + candidates.tsv + name_corrections.tsv + manual_curation.tsv + per-term unresolvable notes from outputs/definitions/*.json. Should be moved into merge_definitions.py as an aggregated report writer (follow-up). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Three new columns make curator review substantially faster: - mapped_label: human-readable label of the mapped UBERON term (looked up from src/ontology/uberon-edit.obo). For new terms, shows '(new term: <label>)'. Saves the curator from having to look up each UBERON ID separately. - parent_correction_label: human-readable label for parent_correction. Same rationale. - mapping_evidence: synthesised evidence from per-term JSON outputs explaining WHY each source term maps to its existing UBERON match. Pulls from various agent field names (note, match_notes, match_evidence, web_evidence, rationale, matched_synonyms). Example: 'UBERON:0035831 has EXACT synonym "costal part of diaphragm" (FMA:58277). The source label "respiratory diaphragm muscle" resolves to UBERON:0001103 (diaphragm)...' Stats: - 71/75 rows have mapped_label populated - 29 confirmed_match rows have mapping_evidence (the other 10 had agents that didn't emit the optional evidence fields — minor gap) - 34 with parent_correction (so 34 with parent_correction_label too) Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Claude finished @dosumis's task in 6m 48s —— View job PR Review: Add HRA Muscular NTR (Third review)Tasks:
Review checklist:
SummaryNo issues from the previous review have been fixed. The three most recent commits ( Additionally, the new NTR terms are not present in The uberon-edit.obo changes in this PR (removing UBERON:1200004 and updating lymph node sinus axioms) appear correct; CI confirms no regression in inferred subclasses for the two affected terms. 🔴 CRITICAL (same as previous review — still unresolved)1. Templates not registered in ODK config or Makefile
In - filename: hra_muscular.owl
templates:
- hra-muscular-muscle.template.tsv
- hra-muscular-groups.template.tsvAnd a corresponding build rule in 2. EC axiom collision in groups template — three back-layer groupings will be inferred equivalent
All three produce the identical EquivalentClass axiom 🟡 IMPORTANT (same as previous review — still unresolved)3. ASCTB-TEMP IRIs still in the All 33 terms still carry 4. Neither template has a 5. The reports directory now has 6 files ( 6. Three leaf terms use
All other skeletal muscle leaf terms in the same template use 7. UBERON:9900025 (lateral compartment of leg muscle) — The definition says "A skeletal muscle organ that is part of the lateral (fibular) fascial compartment of the leg". The 🔵 SUGGESTIONS (carried from previous review)8. ISBN:9780323393225 in def_xref is non-standard — the TA2 URL already covers the Terminologia Anatomica reference; the ISBN could be dropped or moved to a comment. 9. UBERON:9900047 (posterior abdominal wall muscle) — uses What changed since the last reviewThe three newest commits add pipeline output enhancements:
These are valuable workflow additions, but do not address any of the open issues. The uberon-edit.obo changes (removal of UBERON:1200004 and related axiom updates) look correct; CI reports no inferred-subclass regressions for the two affected lymph node sinus terms. Per-template verdict (unchanged)Leaf template (25 terms): Definition quality is high with good PMID support. Specific concerns remain on UBERON:9900003, 9900010, 9900026 (is_a too broad) and UBERON:9900025 (part_of blank). Groups template (8 terms): The critical EC axiom collision on the three back-layer groupings (UBERON:9900020, 9900055, 9900063) must be fixed. The other five groupings (ear, abdominal wall, sole, thoracic wall, middle ear) each have unique locations and are logically sound. The two critical blockers (build registration; EC axiom collision) and the important issues must be addressed before merge. |
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Two critical blockers remain unresolved since the previous review:
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Templates not registered in ODK config/Makefile — hra-muscular-muscle.template.tsv and hra-muscular-groups.template.tsv are absent from uberon-odk.yaml and uberon.Makefile. All 33 new NTR terms exist only in unregistered template files and will never compile into the ontology.
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EC axiom collision in groups template — intermediate back muscle (UBERON:9900020), segmental back muscle (UBERON:9900055), and superficial back muscle (UBERON:9900063) produce identical EquivalentClass axioms (skeletal muscle organ AND part_of dorsum). The reasoner will infer all three are equivalent classes. Change EC to SC for grouping rows.
Also still outstanding (flagged in both prior reviews): ASCTB-TEMP IRIs in def_xref; term_tracker_item missing from both templates; hra-muscular-reports/ under src/templates/; three leaf terms (9900003, 9900010, 9900026) using too-broad is_a UBERON:0001630; UBERON:9900025 part_of column empty.
No issues from the previous review were addressed in the three most recent commits. See the full review comment for details.
- uberon-odk.yaml: add hra_muscular.owl component product, built from hra-muscular-groups.template.tsv + hra-muscular-muscle.template.tsv - update_repo regenerated src/ontology/Makefile (OTHER_SRC, recreate-components, $(COMPONENTSDIR)/hra_muscular.owl rule) and the components documentation page - uberon.Makefile: override the ODK-generated rule for hra_muscular.owl so it pulls in templates/hra-muscular-prefixes.owl (declaring dcterms: and foaf: annotation properties) plus explicit --prefix flags; modelled on the existing hra_skeleton override - templates/hra-muscular-prefixes.owl: new prefix stub declaring all annotation/object properties used in the two muscular template TSVs - catalog-v001.xml: add catalog entry for hra_muscular.owl - uberon-edit.obo: add import: line for the new component - components/hra_muscular.owl: initial generated component file - .github/workflows/diff.yml: change COMP=false -> COMP=true in both classify_branch and classify_main so the #gogoeditdiff workflow rebuilds template-derived components before classification. Without this, PRs that only edit a template TSV produce a no-op classification diff because both sides load the committed component. This lets #gogoeditdiff surface the effect of template changes on both the unreasoned edit-file diff (catalog-resolved imports load the freshly generated component) and the reasoned -base diff. Signed-off-by: @dragon-ai-agent
PR Review: Add HRA Muscular NTR (Fourth review)
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…dit file Adds three HRA back-muscle grouping terms to uberon-edit.obo with plain is_a parents under UBERON:0004469 (musculature of back): - UBERON:9900020 intermediate back muscle - UBERON:9900055 segmental back muscle - UBERON:9900063 superficial back muscle These were originally in hra-muscular-groups.template.tsv with EC axioms of the form (skeletal muscle organ AND part_of some dorsum). Because all three share the same genus + location, the reasoner produced an unsatisfiable triplet collapsing them into a single equivalence class. Per Wikipedia (Human_back), the three groupings are differentiated by anatomical layer, innervation source (anterior vs posterior rami), embryological origin, and function - none of which the simple genus + part_of location pattern can capture. The terms are therefore curated manually as named groupings without OWL equivalence axioms; the rationale is captured in per-term comments and in src/templates/hra-muscular-reports/manual_curation.tsv. Refs #3707 Signed-off-by: @dragon-ai-agent Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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#gogoedtidiff |
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Claude finished @dosumis's task in 5m 21s —— View job PR Review: Add HRA Muscular NTR (Fourth review)Review checklist:
Tasks:
SummaryBoth previous critical blockers are now resolved:
Five important issues from prior reviews remain open: 🟡 IMPORTANT (still outstanding)1. ASCTB-TEMP IRIs still in the All 25 leaf terms and 5 group terms still carry 2. Three leaf terms use
All three are clearly skeletal muscles. All other leaf terms in the same template use 3. UBERON:9900025 (lateral compartment of leg muscle) — The definition says "part of the lateral (fibular) fascial compartment of the leg" but the 4. The three manually-curated terms in 5. Six pipeline-output files remain in 🔵 SUGGESTIONS6. 7. UBERON:9900047 (posterior abdominal wall muscle) uses generic What changed since the last review
Both critical blockers are resolved. The five remaining important issues are convention and logical-accuracy items that should be fixed before merge. |
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Review checklist:
- Hierarchy and parents are consistent (with exceptions noted)
- Definitions and supporting references look adequate
- Obsolete or replacement handling is safe
- OBO and ODK conventions appear preserved — partially (templates now registered ✅; ASCTB-TEMP still in def_xref; term_tracker_item still absent from templates)
- No obvious CI, auth, or workflow regression
Summary: Fourth Review
Both previous critical blockers are now resolved:
-
✅ Templates registered (commit 3f73ed6):
hra-muscular-muscle.template.tsvandhra-muscular-groups.template.tsvare now registered inuberon-odk.yamlanduberon.Makefile, with a prefixes stub and catalog entry. The 33-term component will compile correctly. -
✅ EC axiom collision fixed (commit c21556f): The three identical EC-axiom back-muscle groupings (UBERON:9900020 intermediate, UBERON:9900055 segmental, UBERON:9900063 superficial) were removed from the template and added to
uberon-edit.oboas manually-curated terms with plainis_a UBERON:0004469(musculature of back), well-written rationale comments, andterm_tracker_itemlinks. This is the right approach.
Five important issues from prior reviews remain unresolved:
🟡 IMPORTANT (still outstanding)
1. ASCTB-TEMP IRIs still in the def_xref column
All 25 leaf terms and 5 group terms still carry https://purl.org/ccf/ASCTB-TEMP_<label> in the def_xref column (mapped to oboInOwl:hasDbXref on the definition annotation). These ephemeral workflow-tracking IRIs are being asserted as definition sources. By contrast, the three manually-curated back-muscle terms correctly place the ASCTB-TEMP IRI in the xref: field, not in the definition's xrefs. The template rows should follow the same convention.
2. Three leaf terms use is_a UBERON:0001630 (muscle organ) instead of UBERON:0014892 (skeletal muscle organ, vertebrate)
| NTR ID | Label |
|---|---|
| UBERON:9900003 | articularis genu muscle |
| UBERON:9900010 | dorsal part of intertransversarii laterales lumborum muscle |
| UBERON:9900026 | lateral posterior cervical intertransversarii muscle |
All three are clearly skeletal muscles. All other skeletal-muscle leaf terms in the same template correctly use UBERON:0014892. The inconsistency means these three will not be classified as vertebrate skeletal muscles by the reasoner.
3. UBERON:9900025 (lateral compartment of leg muscle) — part_of column is empty
The definition explicitly states the structure is 'part of the lateral (fibular) fascial compartment of the leg', but the part_of column (column 6) has no value, leaving the textual and logical definitions misaligned. The lateral compartment of leg (UBERON:0035526 is already referenced in the innervated_by column so the IRI is known; the correct part_of target may be a fascial compartment term if one exists, otherwise the current innervated_by reference suggests the compartment IRI needs checking.)
4. term_tracker_item missing from both template files
The three manually-curated terms in uberon-edit.obo correctly have property_value: term_tracker_item "https://github.com/obophenotype/uberon/issues/3707" xsd:anyURI. The remaining 30 template-derived terms do not, because neither template has a term_tracker_item column. Per CLAUDE.md convention these should link back to the originating issue.
5. hra-muscular-reports/ still under src/templates/
Six pipeline-output files (candidates.tsv, errors.tsv, input.tsv, manual_curation.tsv, name_corrections.tsv, review.tsv) remain in src/templates/hra-muscular-reports/. Any tool iterating src/templates/**/*.tsv will treat them as ROBOT templates. These belong in bulk_ntr_workflow/outputs/ or a similar non-template location.
🔵 SUGGESTIONS (carried from prior reviews)
6. ISBN:9780323393225 in def_xref — the TA2 URL already covers the Terminologia Anatomica source; the ISBN is non-standard in OBO/UBERON and could be dropped or moved to a comment.
7. UBERON:9900047 (posterior abdominal wall muscle) — uses generic UBERON:0003697 (abdominal wall) as location; a posterior abdominal wall region term would be more precise if one exists.
What changed since the last review
| Commit | What it does | Issues addressed |
|---|---|---|
3f73ed6 |
Register hra_muscular component; update Makefile, catalog, ODK config; add prefixes stub; enable COMP=true in diff workflow | ✅ Critical #1 fixed |
c21556f |
Move 3 back-muscle groupings to manual curation in uberon-edit.obo | ✅ Critical #2 fixed |
bb73ff6 / 77fd128 / 0fdd84d |
Pipeline report enhancements only | No review issues addressed |
Per-term verdict
Manually-curated back-muscle groupings (uberon-edit.obo):
| NTR | Label | Status |
|---|---|---|
| UBERON:9900020 | intermediate back muscle | ✅ Correctly curated with is_a, comment, term_tracker_item |
| UBERON:9900055 | segmental back muscle | ✅ Same |
| UBERON:9900063 | superficial back muscle | ✅ Same |
Groups template (5 remaining terms):
| NTR | Label | Status |
|---|---|---|
| UBERON:9900013 | external ear muscle | ✅ Unique EC axiom, sound |
| UBERON:9900036 | middle ear muscle | ✅ Unique EC axiom, sound |
| UBERON:9900047 | posterior abdominal wall muscle | 🔵 Generic location (suggestion only) |
| UBERON:9900056 | sole of foot muscle | ✅ Unique EC axiom, sound |
| UBERON:9900068 | thoracic wall muscle | ✅ Unique EC axiom, sound |
Leaf template (25 terms): Definitions and PMIDs are high quality. Specific concerns:
| NTR | Issue |
|---|---|
| UBERON:9900003 | is_a too broad (muscle organ, not skeletal muscle organ vertebrate) |
| UBERON:9900010 | is_a too broad (same) |
| UBERON:9900025 | part_of column blank despite definition describing compartment membership |
| UBERON:9900026 | is_a too broad (same) |
The two critical blockers are resolved — good progress. The remaining issues are important conventions (definition xref semantics, is_a parent precision, term_tracker_item traceability) that should be fixed before merge.
…orts out of templates Addresses review feedback items 3, 4, 5, 7: - Item 3: UBERON:9900025 (lateral compartment of leg muscle) now has part_of UBERON:0000978 (leg). The reviewer's note that 0035526 was in innervated_by was correct — 0035526 is the superficial fibular nerve (not the compartment). No 'lateral compartment of leg' region term exists in UBERON, so the generic 'leg' was used. - Item 4: Both templates now carry a term_tracker_item column (AT IAO:0000233^^xsd:anyURI) pointing back to issue #3707, and hra-muscular-prefixes.owl declares IAO_0000233. All 30 template- derived terms now have term_tracker_item annotations matching the three manually-curated terms. - Item 5: Moved hra-muscular-reports/ from src/templates/ to bulk_ntr_workflow/outputs/. These are pipeline outputs, not ROBOT templates, and were at risk of being picked up by any tooling that iterates src/templates/. Updated generate_template.py, merge_definitions.py, and bulk_ntr_workflow/CLAUDE.md accordingly. - Item 7: posterior abdominal wall (UBERON:9900047): no posterior counterpart of anterior abdominal wall (UBERON:0006635) exists in UBERON, so the term retains its location as the generic abdominal wall (UBERON:0003697). Flagged in manual_curation.tsv for future follow-up. Regenerated src/ontology/components/hra_muscular.owl from the updated templates. Refs #3707 Signed-off-by: @dragon-ai-agent Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
PR Review: Add HRA Muscular NTR (Fifth review)
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Since the three back-muscle grouping terms are curated manually without
OWL equivalence axioms, their member muscles need explicit is_a edges to
populate the hierarchy under each group.
Changes:
- Re-parented all three groupings from UBERON:0004469 (musculature of
back, collection-class) to UBERON:0002324 (muscle of back, singular)
to match UBERON convention for sibling 'X back muscle' terms
(UBERON:0008242 lower / 0008243 upper). This avoids the type mismatch
of asserting a single muscle is_a a musculature.
- Tweaked all three definitions to fit singular interpretation:
'A muscle of back that is part of the [layer]...'. Members are
listed within the definitions and comments make the wiring explicit.
- Added is_a links to existing UBERON members:
UBERON:0002380 trapezius muscle → 9900063 superficial
UBERON:0001112 latissimus dorsi muscle → 9900063 superficial
UBERON:0005461 levator scapulae muscle → 9900063 superficial
UBERON:0001126 serratus dorsalis superior → 9900020 intermediate
UBERON:0001127 serratus dorsalis inferior → 9900020 intermediate
UBERON:8410070 levator costarum → 9900055 segmental
- Re-parented 11 HRA segmental leaf rows in hra-muscular-muscle.template.tsv
from generic UBERON:0014892 / 0001630 / 0004518 to UBERON:9900055
(segmental back muscle): the various interspinales, intertransversarii,
and levatores costarum subdivisions.
Rhomboid major and rhomboid minor have no UBERON terms; not wired here.
Refs #3707
Signed-off-by: @dragon-ai-agent
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…ing EC
UBERON had `anterior abdominal wall` (UBERON:0006635) but no `posterior
abdominal wall`, even though UBERON:0006635's own definition explicitly
partitions the wall into anterior/posterior/lateral. This blocked a
clean Aristotelian EC for the HRA muscular grouping term
`posterior abdominal wall muscle` (UBERON:9900047), which had been
falling back to `part_of abdominal wall` (UBERON:0003697) — too broad
and inconsistent with the parallel anterior wall pattern.
Changes:
- New term UBERON:9900100 `posterior abdominal wall`:
- is_a UBERON:0000475 (organism subdivision)
- part_of UBERON:0003697 (abdominal wall)
- Mirrors UBERON:0006635 (anterior abdominal wall) as the dorsal
sibling subdivision; refs Wikipedia:Abdominal_wall + Gray's
(ISBN:9780323393225).
- Carries the standard added_by_HRA metadata (dc-contributor,
dcterms-date, term_tracker_item, present_in_taxon NCBITaxon:9606,
created_by: dragon-ai-agent).
- Rewire existing posterior-wall muscles with part_of UBERON:9900100:
- UBERON:0001220 quadratus lumborum (already had the synonym
"muscle of posterior abdominal wall" — clear signal it belonged)
- UBERON:0001298 psoas major muscle
- UBERON:0001372 psoas minor muscle
- UBERON:0001369 iliacus muscle
(Per Gray's classification of posterior abdominal wall muscles.)
- Update template hra-muscular-groups.template.tsv row for
UBERON:9900047 `posterior abdominal wall muscle`:
- location -> UBERON:9900100 (was UBERON:0003697)
- Definition reworded to Aristotelian form
"A skeletal muscle organ that is part of a posterior abdominal
wall. Examples: …", mirroring UBERON:0002461 `anterior abdominal
wall muscle` (the existing parallel).
This produces a clean EquivalentClasses axiom in the rebuilt
component: UBERON:9900047 = UBERON:0014892 ∩ part_of UBERON:9900100.
- Rebuilt components/hra_muscular.owl via the make rule (the file now
has the proper ontology IRI Ontology(...components/hra_muscular.owl>
rather than the empty <Ontology/> introduced by an earlier manual
rebuild — fixes Protégé catalog resolution).
After classification the four part_of'd muscles should be inferred as
subclasses of UBERON:9900047 via the EC; downstream PRs can tighten
their muscle-class hierarchy as needed (psoas major/minor/iliacus
currently reach UBERON:0014892 only via deeper chains).
Signed-off-by: @dragon-ai-agent
…e/uberon into add-hra-muscular-ntr
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Claude finished @dosumis's task in 5m 23s —— View job PR Review: Add HRA Muscular NTR (Fifth review)Review checklist:
Tasks:
SummarySignificant progress since the fourth review. Three important issues flagged in previous reviews are now resolved, two back-muscle is_a problems were fixed via re-parenting through ✅ Fixed since the fourth review
🟡 IMPORTANT (still unresolved — flagged in all prior reviews)1. ASCTB-TEMP IRIs still in the All 30 template-derived terms (25 leaf + 5 grouping) still carry For example, By contrast, the three manually-curated back-muscle groupings in 2. UBERON:9900003 (articularis genu muscle) — Row 4 of 🔵 SUGGESTIONS3. UBERON:9900100 (posterior abdominal wall) — no PMID citation The new term's definition cites 4. Iliacus (UBERON:0001369) wired to UBERON:9900100 Adding 5. ISBN references are not standard OBO/UBERON citation form. The TA2 URL ( What changed since the last review
Per-term verdict (current state)Groups template (5 remaining):
Manually-curated back groupings (uberon-edit.obo):
Leaf template (25 terms) — remaining concern:
The two prior critical blockers are resolved, three previously-important issues are now fixed, and the PR is close to ready. Addressing the two remaining important items (ASCTB-TEMP def_xref semantics and the articularis genu is_a) would bring the templates fully in line with Uberon conventions. |
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Fifth review summary
Two important issues from previous reviews remain unresolved:
-
ASCTB-TEMP IRIs still in the
def_xrefcolumn — all 30 template-derived terms assert ephemeral workflow-tracking IRIs (https://purl.org/ccf/ASCTB-TEMP_...) as definition sources. The manually-curated back-muscle groupings inuberon-edit.obocorrectly place these in thexref:field instead. The template rows should follow the same pattern. -
UBERON:9900003 (articularis genu muscle) —
is_a UBERON:0001630(muscle organ) instead ofUBERON:0014892(skeletal muscle organ, vertebrate). All other skeletal muscle leaf terms in the template now useUBERON:0014892or a more specific parent; this one remains inconsistent.
Both blockers from the fourth review are resolved, and three previously-important items are now fixed (part_of for 9900025 ✅, term_tracker_item column ✅, reports moved out of src/templates ✅). The two back-muscle is_a problems (9900010, 9900026) are also fixed via re-parenting through UBERON:9900055, and the new UBERON:9900100 (posterior abdominal wall) provides a clean EC location for UBERON:9900047. Excellent progress — two small fixes to go.
…ange) The 9900000-10000000 range is reserved for temporary IDs that are reassigned on merge to master. It is only appropriate for terms added directly to uberon-edit.obo, not for template-driven terms. Remapped 30 template-row IDs from UBERON:99xxxxx to UBERON:1100001-1100030 (David Osumi-Sutherland range), preserving sort order: 9900001->1100001 9900003->1100002 9900008->1100003 9900010->1100004 9900013->1100005 9900015->1100006 9900018->1100007 9900019->1100008 9900022->1100009 9900023->1100010 9900025->1100011 9900026->1100012 9900030->1100013 9900031->1100014 9900034->1100015 9900035->1100016 9900036->1100017 9900037->1100018 9900038->1100019 9900039->1100020 9900047->1100021 9900049->1100022 9900050->1100023 9900056->1100024 9900061->1100025 9900062->1100026 9900064->1100027 9900067->1100028 9900068->1100029 9900074->1100030 The four UBERON:99xxxxx terms in uberon-edit.obo (9900020 intermediate back muscle, 9900055 segmental back muscle, 9900063 superficial back muscle, 9900100 posterior abdominal wall) stay in the temp range - those are direct ontology terms and will be reassigned on merge per the standard temp-ID protocol. Files updated: - src/templates/hra-muscular-muscle.template.tsv: 25 row IDs remapped - src/templates/hra-muscular-groups.template.tsv: 5 row IDs remapped - bulk_ntr_workflow/outputs/hra-muscular-reports/manual_curation.tsv - bulk_ntr_workflow/outputs/hra-muscular-reports/review.tsv Also regenerated src/ontology/components/hra_muscular.owl using the full Makefile rule (template + annotate ontology-iri/version-iri/version + convert -f ofn). This fixes prior commits that had written the file in RDF/XML with an empty <Ontology/> annotation block. Refs #3707 Signed-off-by: @dragon-ai-agent Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
… 'foaf:depiction' The illegal-annotation-property-violation.sparql check was failing on <http://purl.obolibrary.org/obo/foaf_depiction> — a malformed IRI produced because uberon-edit.obo doesn't declare the foaf prefix in its header, so robot interpreted 'foaf:depiction' as a CURIE resolving to obo:foaf_depiction. uberon-edit.obo already declares a Typedef: [Typedef] id: depiction name: depiction xref: http://xmlns.com/foaf/0.1/depiction is_metadata_tag: true so the established convention (1887 existing uses) is 'property_value: depiction "..." xsd:anyURI', which resolves correctly to the real foaf:depiction IRI (allowlisted in the QC). Rewrote the three back-muscle grouping stanzas (UBERON:9900020/9900055/9900063) to use the 'depiction' shortcut instead of 'foaf:depiction'. Refs #3707 Signed-off-by: @dragon-ai-agent Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
… muscle organ Two fixes: 1. Convert ASCTB-TEMP tracking IRIs to ccf:-prefixed CURIEs Previously stored as full URLs like https://purl.org/ccf/ASCTB-TEMP_articularis-genu-muscle in def_xrefs. Now stored as ccf:ASCTB-TEMP_articularis-genu-muscle. - uberon-edit.obo: added 'idspace: ccf https://purl.org/ccf/' header declaration and rewrote 3 xrefs in the back-muscle grouping terms - hra-muscular-muscle.template.tsv: rewrote 25 xrefs - hra-muscular-groups.template.tsv: rewrote 5 xrefs - hra-muscular-prefixes.owl: declared Prefix(ccf:=<https://purl.org/ccf/>) - src/ontology/uberon.Makefile: added --prefix "ccf: https://purl.org/ccf/" to the hra_muscular component template rule 2. UBERON:1100002 articularis genu muscle: re-parent from UBERON:0001630 (muscle organ) to UBERON:0014892 (skeletal muscle organ, vertebrate), matching the genus used by other skeletal muscle terms in the template. Component owl regenerated via the full template + annotate + convert pipeline. Refs #3707 Signed-off-by: @dragon-ai-agent Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Claude finished @dosumis's task in 6m 3s —— View job PR Review: Add HRA Muscular NTR (Sixth review)Review checklist:
Tasks:
SummaryExcellent progress in this sync — four open issues from the fifth review are now resolved. Two small issues remain before merge. ✅ Fixed since the fifth review
🟡 IMPORTANT (still outstanding)1. ASCTB-TEMP CURIEs still in the Commit 2. UBERON:9900100 (posterior abdominal wall) — missing Per CLAUDE.md, new manually-curated terms require 🔵 SUGGESTIONS3. 4. UBERON:9900100 definition cites only Per-term verdict (current state)Manually-curated terms (uberon-edit.obo):
Groups template (5 terms): ✅ Unique EC axioms, proper parents, good definitions. Leaf template (25 terms): ✅ All is_a parents correct. ASCTB-TEMP in def_xref (shared with groups) is the only remaining issue. The two prior critical blockers are resolved. All five previously-important issues except the ASCTB-TEMP placement and the new dc-contributor gap are fixed. Two small changes remain. |
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Sixth review summary
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 — mostly (ASCTB-TEMP still in def_xref; dc-contributor missing on UBERON:9900100)
- No obvious CI, auth, or workflow regression
✅ Fixed since the fifth review
Four issues resolved in commits de0719b, 58c9677, and 692925c:
| Issue | Commit | Status |
|---|---|---|
| UBERON:9900003 (articularis genu) — is_a too broad | de0719b | ✅ Now is_a UBERON:0014892 (skeletal muscle organ, vertebrate) |
| ASCTB-TEMP full IRIs in def_xref | de0719b | ✅ Converted to ccf: CURIEs; idspace ccf declared in uberon-edit.obo header; back-muscle grouping xrefs corrected |
| foaf:depiction in uberon-edit.obo back-muscle stanzas | 58c9677 | ✅ Rewrote to use established 'depiction' OBO shortcut |
| Template IDs in 99xxxxx temp range | 692925c | ✅ Reassigned 30 template terms to UBERON:1100001-1100030 (David Osumi-Sutherland range); UBERON:1100000 (digestive tract junction) already existed immediately below |
🟡 IMPORTANT (still outstanding)
1. ASCTB-TEMP CURIEs still in the def_xref column — asserted as definition sources
The de0719b fix converted the ASCTB-TEMP tokens from full IRIs to ccf: CURIEs and correctly placed them in the xref: field of the three manually-curated uberon-edit.obo stanzas. However, in both template files all 30 template-derived terms still carry ccf:ASCTB-TEMP_ in the def_xref column (>A oboInOwl:hasDbXref SPLIT=|). This asserts the ASCTB-TEMP CURIEs as annotations on the definition annotation — i.e., as sources for the definition text — which is semantically incorrect for workflow-tracking identifiers. They should be moved to the general xref column (A oboInOwl:hasDbXref SPLIT=|, column 18 in the muscle template) instead.
Confirmed in hra_muscular.owl (e.g. line 125):
The ccf:ASCTB-TEMP token appears inside the annotation qualifiers on the definition — not as a standalone class xref.
2. UBERON:9900100 (posterior abdominal wall) — missing dc-contributor
Per CLAUDE.md, new manually-curated terms require:
The other three manually-curated back-muscle grouping terms (UBERON:9900020, 9900055, 9900063) all have this. UBERON:9900100 has dcterms-date and term_tracker_item but not dc-contributor. Given the pattern on all other new terms in this PR, it should be:
🔵 SUGGESTIONS
3. ISBN:9780323393225 in def_xref columns is non-standard for OBO/UBERON citation; the TA2 URL already covers the Terminologia Anatomica reference and the ISBN could be dropped or moved to a comment.
4. UBERON:9900100 has no PMID — only ISBN and Wikipedia. This matches the pattern on UBERON:0006635 (anterior abdominal wall) so it is not a blocker, but a supporting PMID would strengthen the definition.
Per-term verdict (current state)
Manually-curated back groupings and posterior abdominal wall (uberon-edit.obo):
| NTR | Label | Status |
|---|---|---|
| UBERON:9900020 | intermediate back muscle | ✅ |
| UBERON:9900055 | segmental back muscle | ✅ |
| UBERON:9900063 | superficial back muscle | ✅ |
| UBERON:9900100 | posterior abdominal wall | 🟡 missing dc-contributor |
Groups template (5 terms, UBERON:1100005/1100017/1100021/1100024/1100029): ✅ Unique EC axioms, proper parents, good definitions.
Leaf template (25 terms, UBERON:1100001-1100030 subset): Definition quality remains high with good PMID support. All previous is_a issues resolved. Only residual issue: ASCTB-TEMP in def_xref (all 30 template terms).
The PR is very close to ready. Two small fixes remain.
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Sixth review summary
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 — mostly (ASCTB-TEMP still in def_xref; dc-contributor missing on UBERON:9900100)
- No obvious CI, auth, or workflow regression
Fixed since the fifth review
Four issues resolved in commits de0719b, 58c9677, and 692925c:
| Issue | Commit | Status |
|---|---|---|
| UBERON:9900003 (articularis genu) is_a too broad | de0719b | Fixed — now is_a UBERON:0014892 (skeletal muscle organ, vertebrate) |
| ASCTB-TEMP full IRIs in def_xref | de0719b | Converted to ccf: CURIEs; idspace ccf declared in uberon-edit.obo; back-muscle grouping xrefs corrected |
| foaf:depiction in uberon-edit.obo back-muscle stanzas | 58c9677 | Rewrote to use established 'depiction' OBO shortcut |
| Template IDs in 99xxxxx temp range | 692925c | Reassigned 30 template terms to UBERON:1100001-1100030 |
IMPORTANT (still outstanding)
1. ASCTB-TEMP CURIEs still in the def_xref column
The de0719b fix correctly placed ASCTB-TEMP in the xref: field of the three manually-curated uberon-edit.obo stanzas. However, in both template files all 30 template-derived terms still carry ccf:ASCTB-TEMP_ in the def_xref column (>A oboInOwl:hasDbXref SPLIT=|), asserting them as annotation qualifiers on the definition — i.e., sources of the definition text. They should be in the general xref column (A oboInOwl:hasDbXref SPLIT=|, column 18 in the muscle template) instead. Confirmed in hra_muscular.owl line 125 where ccf:ASCTB-TEMP_anterior-cervical... appears inside the definition's annotation qualifiers.
2. UBERON:9900100 (posterior abdominal wall) missing dc-contributor
Per CLAUDE.md, new manually-curated terms require a dc-contributor relationship. UBERON:9900020, 9900055, and 9900063 all have it. UBERON:9900100 has dcterms-date and term_tracker_item but not dc-contributor. Should add: relationship: dc-contributor https://orcid.org/0000-0002-7073-9172 ! David Osumi-Sutherland
Suggestions
- ISBN:9780323393225 in def_xref is non-standard for OBO/UBERON; the TA2 URL already covers the Terminologia Anatomica reference.
- UBERON:9900100 has no PMID (only ISBN and Wikipedia); a supporting PMID would strengthen the definition.
The PR is very close to ready — two small fixes remain.
Reasoning the merged ontology produced 8 unsatisfiable classes — all deep back muscles in hra-muscular-muscle.template.tsv: UBERON:1100001 anterior cervical intertransversarii muscle UBERON:1100010 intertransversarii laterales lumborum muscle UBERON:1100015 medial lumbar intertransversarii muscle UBERON:1100016 medial posterior cervical intertransversarii muscle UBERON:1100018 multifidus cervicis muscle UBERON:1100019 multifidus lumborum muscle UBERON:1100020 multifidus thoracis muscle UBERON:1100028 thoracic intertransversarii muscle robot explain identified the same clash for each: each was asserted SubClassOf `part of some <cervical/thoracic/lumbar region of vertebral column>` (UBERON:0006072/3/4). Those terms propagate part_of into `postcranial axial skeleton` -> `subdivision of skeleton` -> `skeleton`. The genus path (skeletal muscle organ, vertebrate) propagates the muscle into `part of some musculature of body`. UBERON ships a disjointness: part_of some musculature_of_body DisjointWith part_of some skeleton …hence unsat. A muscle attaches to the spine, but is not part of it. Fix — match the convention used by `axial muscle` (UBERON:0003897), which uses `attaches_to_part_of` (RO:0002177) for the skeletal target and reserves `part_of` for a body region: - Added an `attaches_to_part_of` column to hra-muscular-muscle.template.tsv (header `SC RO:0002177 some %`, inserted after `part_of`). - For the 8 affected rows: moved the spine-region UBERON ID from `part_of` to `attaches_to_part_of`, and set `part_of` to UBERON:0001137 `dorsum` (the canonical body region for back muscles — same filler used by the EC of UBERON:0002324 `muscle of back`, the inherited grouping for these terms). - Rebuilt components/hra_muscular.owl via the make rule. Verified end-to-end with the failing pipeline: robot ... expand --no-expand-term RO_0002175 -o tmp/uberon-edit.owl robot ... merge ... bridge/uberon-bridge-to-bfo.owl relax reason -r elk …now completes with 0 unsatisfiable classes. The cervical/thoracic/lumbar spinal-level information is preserved (now in `attaches_to_part_of`), and the muscles are still grouped under `muscle of back` via genus inheritance. Signed-off-by: @dragon-ai-agent
The previous commit added an attaches_to_part_of (RO:0002177) column to hra-muscular-muscle.template.tsv but did not declare RO:0002177 in templates/hra-muscular-prefixes.owl. robot template auto-typed the unknown CURIE as a DataProperty, emitting 8 bogus axioms like: Declaration(DataProperty(RO_0002177)) Declaration(Datatype(UBERON_0006072)) Declaration(Datatype(UBERON_0006073)) Declaration(Datatype(UBERON_0006074)) SubClassOf(UBERON_1100018 DataSomeValuesFrom(RO_0002177 UBERON_0006072)) …which then made the merged ontology blow up in the release pipeline: Cannot pun between properties: <RO_0002177> Datatype IRI also used as Class IRI: <UBERON_0006072> Datatype IRI also used as Class IRI: <UBERON_0006073> Fix: add `Declaration(ObjectProperty(<RO_0002177>))` to hra-muscular-prefixes.owl. The rebuilt component now contains the correct `ObjectSomeValuesFrom(RO_0002177 ...)` axioms, with the cervical/thoracic/lumbar region of vertebral column IRIs treated as Classes (not Datatypes). Verified: - reason_test (ELK, --equivalent-classes-allowed asserted-only, --exclude-tautologies structural): PASS, 0 unsatisfiable classes. - sparql_test (9 violation queries): all PASS, 0 violations. This is the same trap the hra_skeleton template avoids by declaring its object/annotation properties up front in hra-skeleton-prefixes.owl. Both prefix stubs now follow the same pattern. Signed-off-by: @dragon-ai-agent
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Claude finished @dosumis's task in 3m 58s —— View job PR Review: Add HRA Muscular NTR (Seventh review)Review checklist:
Tasks:
SummaryTwo new commits since the sixth review address a critical reasoning problem that was blocking the release pipeline. One issue from the sixth review was a false alarm. One important convention issue remains. ✅ Fixed since the sixth review
The reasoning fix ( Sixth review issue #2 (UBERON:9900100 dc-contributor) was a false alarm. The current stanza shows 🟡 IMPORTANT (still unresolved — flagged in all six prior reviews)1. ASCTB-TEMP CURIEs still in the Both template files still carry The fix: remove the The three manually-curated 🔵 SUGGESTIONS (carried from prior reviews)
What changed since the last review
Per-term verdict (current state)Manually-curated terms (uberon-edit.obo): All four (UBERON:9900020, 9900055, 9900063, 9900100) ✅ — correct Groups template (5 terms, UBERON:1100005/1100017/1100021/1100024/1100029): ✅ Unique EC axioms, proper parents, good definitions. Only shared issue is ASCTB-TEMP in def_xref. Leaf template (25 terms, UBERON:1100001–1100030 subset): ✅ All is_a parents correct; One small fix remains. |
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Seventh review summary
Two new commits since the sixth review fix a critical reasoning problem and a ROBOT property-typing issue — both important build correctness fixes:
d5f52d5: 8 unsatisfiable classes resolved by addingattaches_to_part_of(RO:0002177) column and moving spine-region IDs out ofpart_of— follows theaxial muscle(UBERON:0003897) convention correctly.2007e30:RO:0002177declared as ObjectProperty in hra-muscular-prefixes.owl, preventing ROBOT from auto-typing it as DataProperty (which caused punning errors in the merged ontology).
The sixth review's issue #2 (UBERON:9900100 missing dc-contributor) was a false alarm — the stanza has had dc-contributor since commit 8117acb.
One important issue remains (flagged in all six prior reviews, still unresolved):
The def_xref column (>A oboInOwl:hasDbXref SPLIT=|) in both template TSV files still contains ccf:ASCTB-TEMP_<label> CURIEs alongside real definition citations. In ROBOT template syntax, >A places values as annotation qualifiers on the definition annotation itself, asserting these ephemeral workflow-tracking IRIs as sources for the definition text. They should be removed from def_xref and placed in the plain xref column (A oboInOwl:hasDbXref SPLIT=|, column 18 in the muscle template, column 14 in the groups template), consistent with how the three manually-curated back-muscle stanzas handle them in uberon-edit.obo.
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Claude finished @dosumis's task in 7m 50s —— View job PR Review: Add HRA Muscular NTR (Eighth review)Review checklist:
Tasks:
SummaryThis review addresses the one remaining issue flagged in all seven prior reviews: ccf:ASCTB-TEMP_ CURIEs used as definition sources instead of plain xrefs. I prepared the fix and committed it locally, but could not push because the Changes prepared (commit
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| Issue | Status |
|---|---|
| Templates not registered in ODK/Makefile | ✅ Fixed in 3f73ed6 |
| EC axiom collision (3 back groupings) | ✅ Fixed in c21556f |
| UBERON:9900008 missing is_a | ✅ Fixed |
| UBERON:9900003 articularis genu is_a too broad | ✅ Fixed in de0719b |
| UBERON:9900010/9900026 is_a too broad | ✅ Fixed in 6436580 |
| UBERON:9900025 part_of column blank | ✅ Fixed in e640036 |
| term_tracker_item missing from templates | ✅ Fixed in e640036 |
| hra-muscular-reports/ under src/templates/ | ✅ Fixed in e640036 |
| 8 unsatisfiable classes (part_of spine region) | ✅ Fixed in d5f52d5 |
| RO:0002177 typed as DataProperty | ✅ Fixed in 2007e30 |
| ASCTB-TEMP CURIEs as definition sources | 🟡 Script above; commit 4041700 prepared but push blocked |
Once this last fix is applied and CI passes, this PR is ready to merge.
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#gogoeditdiff |
1 participant
fixes #3707