Add hra muscular ntr

.claude/agents/ntr-term-researcher.md

@@ -46,6 +46,7 @@ The file contains:
       "ntr_id": "http://purl.obolibrary.org/obo/UBERON_9900001",
       "label": "term label",
       "term_type": "leaf",
+      "system":  "default | muscle",
       "is_a":    "INFER:UBERON:xxxxxxx | NEEDS_MAPPING:FMA:nnnnn | UNRESOLVABLE:...",
       "part_of": "INFER:UBERON:xxxxxxx | ...",
       "def_xref": "ref1|ref2|..."
@@ -183,40 +184,124 @@ For each term without a confirmed existing UBERON match:
 - Where members are known and bounded, enumerate: "...comprising the X, Y, and Z."
 - Length still 20–60 words.
 
-## Step 7: Resolve Relationship Types (LEAF terms only)
-
-For each `term_type: "leaf"` term, determine whether it should be `is_a` or `part_of` the
-resolved parent:
-
-**Use `part_of` when the term is a physical subdivision of the parent:**
-- Named **layer**, zone, region, wall, surface, border, lumen, stroma, cortex, medulla
-- Named **head**, belly, compartment, lobe, segment, fascicle of a specific named structure
-- Any term where the phrase "is **contained within**", "is **a subdivision of**", or
-  "is **a layer of**" the parent is correct
-- Examples: `corpus luteum granulosa lutein layer` **part_of** corpus luteum;
-  `clavicular head of pectoralis major` **part_of** pectoralis major;
-  `costal part of diaphragm` **part_of** diaphragm;
-  `cumulus oophorus oocyte complex` **part_of** antral follicle
-
-**Use `is_a` when the term is a classification type within the parent category:**
-- The parent is a **grouping class** (e.g. "muscle of neck", "ovarian follicle stage",
-  "cranial muscle") and the term is a **member of that category**
-- The term can be truly described as "IS A [parent]" — i.e. it has all properties of the
-  parent and adds further specificity
-- Examples: `anterior vertebral muscle` **is_a** muscle of neck;
-  `primary ovarian follicle` **is_a** ovarian follicle;
-  `dominant antral follicle` **is_a** antral follicle
-
-**Quick test**: ask "Is a [term] a kind of [parent]?" (→ `is_a`) vs "Is a [term] inside/part
-of a [parent]?" (→ `part_of`). When in doubt, prefer `part_of` for physically bounded
-sub-structures and `is_a` for stages or functional subtypes.
-
-If unclear after applying these rules: search `ols4` for existing children of the same parent
-and check the relationship type they use; apply the same pattern.
-
-Record each decision in `resolved_relationships`. (Skip for `term_type: "group"` —
-relationships for those are encoded as `genus + part_of some Y` equivalent classes;
-see Step 8.)
+## Step 7: Resolve genus AND part_of for LEAF terms
+
+For each `term_type: "leaf"` term, look up how UBERON defines similar specific structures
+to determine BOTH a genus (`is_a`) class AND a `part_of` containing structure. UBERON
+convention typically populates both for specific named anatomical entities — e.g.
+`vastus lateralis` has `is_a: UBERON:0001630 ! muscle organ` AND
+`relationship: part_of UBERON:0001377 ! quadriceps femoris`.
+
+**Procedure:**
+
+1. Use awk over `src/ontology/uberon-edit.obo` to find similar specific UBERON terms.
+   Examples for muscle subdivisions:
+   ```bash
+   awk 'BEGIN{RS=""} /\nname: .*head of .*muscle/' src/ontology/uberon-edit.obo
+   awk 'BEGIN{RS=""} /\nname: .*part of .*muscle/' src/ontology/uberon-edit.obo
+   awk 'BEGIN{RS=""} /\nname: .*belly of/' src/ontology/uberon-edit.obo
+   awk 'BEGIN{RS=""} /\nid: UBERON:0001379\n/' src/ontology/uberon-edit.obo  # vastus lateralis
+   ```
+
+2. From similar terms, extract the genus pattern. Common UBERON genus classes for
+   muscle leaf terms:
+   - `UBERON:0001630` muscle organ — for whole named individual muscles (e.g. articularis
+     genu, longus capitis, vastus lateralis)
+   - `UBERON:0011906` muscle head — for named heads of muscles (clavicular head, long
+     head, short head)
+   - `UBERON:0014892` skeletal muscle organ, vertebrate — for skeletal muscles when a
+     more specific class is unavailable
+   - `UBERON:0014892` or domain-specific (e.g. `UBERON:0001135` smooth muscle organ)
+     for non-skeletal cases
+
+3. From similar terms, extract the part_of pattern. Common targets:
+   - For "X head/belly/part of Y muscle" → part_of the named parent muscle Y
+   - For named muscles in a region → part_of the region (e.g. neck, thigh,
+     anterior compartment)
+   - For named segmental muscles → part_of the relevant region (cervical vertebral
+     column, lumbar region, etc.)
+
+4. Emit a `leaf_template_rows[label]` entry with `{"is_a": "UBERON:...", "part_of":
+   "UBERON:..."}`. **Both columns should be populated when applicable.**
+   - Set `is_a` only (omit `part_of`) for classification subtypes that don't have a
+     containing structure (e.g. `dominant antral follicle is_a antral follicle` — no
+     additional part_of needed beyond what the genus class implies).
+   - Set `part_of` only (omit `is_a` or use a very generic genus) when the term is
+     purely a subdivision and no specific genus class is available.
+
+5. The legacy `resolved_relationships` + `resolved_parents` keys are still accepted as
+   a fallback but `leaf_template_rows` is preferred — it expresses both axes
+   simultaneously.
+
+**Optional fields in `leaf_template_rows` (Phase 6 + 7):**
+
+The default leaf template has an OPTIONAL `develops_from` column. The muscular-system
+overlay also has `has_muscle_origin`, `has_muscle_insertion`, `innervated_by` columns.
+Populate any of these in `leaf_template_rows[label]` when you have evidence:
+
+```json
+"leaf_template_rows": {
+  "early antral follicle": {
+    "is_a": "UBERON:0000037",
+    "develops_from": "UBERON:0000036"
+  },
+  "articularis genu muscle": {
+    "is_a": "UBERON:0001630",
+    "part_of": "UBERON:0000376",
+    "has_muscle_origin": "UBERON:0000981",
+    "has_muscle_insertion": "UBERON:0000976",
+    "innervated_by": "UBERON:0001267"
+  }
+}
+```
+
+The merge step writes any of these to the corresponding column IF the column exists in
+the current template variant. Unknown fields are silently dropped — you don't need to
+know which template the row belongs to. Just emit whatever you can populate with
+evidence.
+
+**Stage-series guidance for `develops_from`:**
+
+For terms in a developmental sequence (follicle stages, embryonic stages, hematopoietic
+differentiation), look up the precursor stage via OLS4 / awk and emit `develops_from`.
+Example: `early antral follicle` develops_from `secondary ovarian follicle`
+(UBERON:0000036).
+
+**Muscle-overlay guidance for `has_muscle_origin`/`has_muscle_insertion`/`innervated_by`:**
+
+For `system: "muscle"` terms (the per-group JSON contains a `system` field per term),
+extract origin/insertion/innervation from Wikipedia + UBERON precedent. The bone or
+nerve labels in Wikipedia text typically need OLS4 lookup to resolve to UBERON IDs
+(e.g. "femur" → UBERON:0000981, "femoral nerve" → UBERON:0001267). If a UBERON ID
+cannot be resolved (named bone landmark, specific nerve branch missing from UBERON),
+omit that field rather than guess.
+
+**Worked examples:**
+
+- `clavicular head of pectoralis major muscle`:
+  - Look up similar: UBERON:0007168 (long head of biceps brachii), UBERON:0007169 (short
+    head of biceps brachii) → both use `is_a: UBERON:0011906 ! muscle head` and
+    `relationship: part_of <named muscle>`.
+  - Emit: `{"is_a": "UBERON:0011906", "part_of": "UBERON:0002381"}`
+
+- `articularis genu muscle`:
+  - Look up similar: vastus lateralis (UBERON:0001379) uses
+    `is_a: UBERON:0001630 ! muscle organ` + `part_of UBERON:0001377 ! quadriceps femoris`.
+  - For articularis genu, the analogous part_of would be the thigh region (or anterior
+    compartment of thigh if a UBERON term exists for it). Emit:
+    `{"is_a": "UBERON:0001630", "part_of": "UBERON:0004252"}` (or more specific).
+
+- `costal part of respiratory diaphragm muscle`: similar UBERON pattern is to use a
+  domain part as `part_of` plus a generic genus. Already a confirmed match in this
+  case (UBERON:0035831), so this term is excluded from the leaf template.
+
+- `dominant antral follicle` (a stage/subtype, no spatial part_of beyond the parent):
+  emit `{"is_a": "UBERON:0000035"}` only — omit `part_of`.
+
+**Important — DO NOT just take the supplied source parent and assign it to one column.**
+Look at similar UBERON terms first; the source parent is often too broad (a grouping class)
+to serve as the genus, and a more specific genus may be obvious (muscle head, muscle
+organ, etc.).
 
 ## Step 8: Group term equivalent class — genus + part_of some Y (GROUP terms only)
 
@@ -288,6 +373,16 @@ Save to: `bulk_ntr_workflow/outputs/definitions/{group_name}.json`
   "def_xrefs_to_add": {
     "term label": "PMID:12345678|PMID:87654321"
   },
+  "leaf_template_rows": {
+    "leaf term label": {
+      "is_a":    "UBERON:0011906",
+      "part_of": "UBERON:0002381",
+      "develops_from":         "UBERON:0000036",
+      "has_muscle_origin":     "UBERON:0001105",
+      "has_muscle_insertion":  "UBERON:0000976",
+      "innervated_by":         "UBERON:0003726"
+    }
+  },
   "resolved_relationships": {
     "leaf term label": "is_a | part_of"
   },
@@ -361,17 +456,28 @@ Omit empty lists/dicts. Do NOT include a `fma_resolutions` key — use `resolved
 - Every confirmed match must have both a UBERON definition and Wikipedia/literature evidence.
 - Every new term must have at least one real PMID/DOI in `def_xrefs_to_add` or in the existing
   `def_xref` input field (ASCTB-TEMP placeholders do not count as real references).
-- `resolved_relationships` values must be `"is_a"` or `"part_of"` only.
-- `resolved_parents` values must be real UBERON IDs retrieved from OLS4 — never guessed.
-- Layers, zones, heads, bellies, parts of named structures → must be `part_of`, never `is_a`.
+- For LEAF terms: prefer emitting `leaf_template_rows[label]` with both `is_a` and
+  `part_of` populated. Look up similar UBERON terms via awk over uberon-edit.obo to
+  find the right genus class — do NOT just assign the source parent to one column.
+- `leaf_template_rows[label].is_a` should be a genus class (e.g. UBERON:0001630 muscle
+  organ, UBERON:0011906 muscle head), not a regional grouping class.
+- `leaf_template_rows[label].part_of` should be the containing structure (parent muscle,
+  body region, compartment).
+- For backward compatibility, `resolved_relationships` (values `"is_a"` or `"part_of"`)
+  + `resolved_parents` may still be used; merge will fall back to these if
+  `leaf_template_rows` is absent.
+- All UBERON ID values must be real UBERON IDs retrieved from OLS4 or uberon-edit.obo —
+  never guessed.
+- Layers, zones, heads, bellies, parts of named structures → MUST have `part_of`
+  populated to the named parent structure.
 - Pathological/dysfunctional terms → must appear in `out_of_scope`.
 - Non-standard names → must appear in `name_corrections`.
 - **For `term_type: "group"` terms**: every term must end up in EITHER
   `group_template_rows` (with both `genus` and `location` populated as real UBERON IDs)
   OR `manual_curation` (with proposed definition + similar UBERON terms). No group term
   should be silently absent from both.
-- `resolved_relationships` and `resolved_parents` apply to LEAF terms only — do not emit
-  these keys for group terms.
+- `leaf_template_rows`, `resolved_relationships`, `resolved_parents` apply to LEAF terms
+  only — do not emit these keys for group terms.
 - Do NOT invent UBERON IDs.
 
 ## Tools Available

.github/workflows/ai-agent.yml

@@ -4,8 +4,7 @@
 # and runs Claude Code to respond.
 #
 # Required secrets:
-# - AI4C_AGENT_APP_ID
-# - AI4C_AGENT_PRIVATE_KEY
+# - PAT_FOR_PR
 # - CLAUDE_CODE_OAUTH_TOKEN
 #
 # Configuration:
@@ -56,24 +55,17 @@ jobs:
     outputs:
       result: ${{ steps.check.outputs.result }}
     steps:
-      - name: Generate ai4c-agent token
-        id: app-token
-        uses: actions/create-github-app-token@v3
-        with:
-          app-id: ${{ secrets.AI4C_AGENT_APP_ID }}
-          private-key: ${{ secrets.AI4C_AGENT_PRIVATE_KEY }}
-
       - name: Checkout repository
         uses: actions/checkout@v6
         with:
           fetch-depth: 1
-          token: ${{ steps.app-token.outputs.token }}
+          token: ${{ secrets.PAT_FOR_PR }}
 
       - name: Check for qualifying mention
         id: check
         uses: actions/github-script@v8
         with:
-          github-token: ${{ steps.app-token.outputs.token }}
+          github-token: ${{ secrets.PAT_FOR_PR }}
           script: |
             const fs = require("fs");
 
@@ -250,22 +242,14 @@ jobs:
       contents: write
       issues: write
       pull-requests: write
-      id-token: write
     runs-on: ubuntu-latest
     container: ${{ fromJSON(needs.check-mention.outputs.result).useOdkContainer && 'obolibrary/odkfull:v1.6' || null }}
     steps:
-      - name: Generate ai4c-agent token
-        id: app-token
-        uses: actions/create-github-app-token@v3
-        with:
-          app-id: ${{ secrets.AI4C_AGENT_APP_ID }}
-          private-key: ${{ secrets.AI4C_AGENT_PRIVATE_KEY }}
-
       - name: Checkout repository
         uses: actions/checkout@v6
         with:
           fetch-depth: 1
-          token: ${{ steps.app-token.outputs.token }}
+          token: ${{ secrets.PAT_FOR_PR }}
 
       - name: Configure Git
         run: |
@@ -294,13 +278,13 @@ jobs:
           echo "${{ github.workspace }}/.venv/bin" >> "$GITHUB_PATH"
 
       - name: Export GitHub token for gh CLI
-        run: echo "GH_TOKEN=${{ steps.app-token.outputs.token }}" >> "$GITHUB_ENV"
+        run: echo "GH_TOKEN=${{ secrets.PAT_FOR_PR }}" >> "$GITHUB_ENV"
 
       - name: Run Claude Code
         uses: anthropics/claude-code-action@v1
         with:
           claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
-          github_token: ${{ steps.app-token.outputs.token }}
+          github_token: ${{ secrets.PAT_FOR_PR }}
           allowed_bots: "claude,github-actions"
           show_full_output: true
           claude_args: |

.github/workflows/diff.yml

@@ -110,7 +110,7 @@ jobs:
           ref: ${{ steps.comment-branch.outputs.head_ref }}
       - name: Classify ontology PR branch
         if: steps.check.outputs.triggered == 'true'
-        run: export ROBOT_JAVA_ARGS='-Xmx9G'; cd src/ontology; make BRI=false MIR=false PAT=false IMP=false COMP=false uberon-base.owl > TESTLOG.log
+        run: export ROBOT_JAVA_ARGS='-Xmx9G'; cd src/ontology; make BRI=false MIR=false PAT=false IMP=false COMP=true uberon-base.owl > TESTLOG.log
       - name: Upload classified ontology in PR branch
         if: steps.check.outputs.triggered == 'true'
         uses: actions/upload-artifact@v4
@@ -136,7 +136,7 @@ jobs:
           ref: master
       - name: Classify ontology main branch
         if: steps.check.outputs.triggered == 'true'
-        run: export ROBOT_JAVA_ARGS='-Xmx9G'; cd src/ontology; make BRI=false MIR=false PAT=false IMP=false COMP=false uberon-base.owl > TESTLOG.log
+        run: export ROBOT_JAVA_ARGS='-Xmx9G'; cd src/ontology; make BRI=false MIR=false PAT=false IMP=false COMP=true uberon-base.owl > TESTLOG.log
       - name: Upload classified ontology main branch
         if: steps.check.outputs.triggered == 'true'
         uses: actions/upload-artifact@v4

bulk_ntr_workflow/CLAUDE.md

@@ -185,12 +185,12 @@ After QC, both templates need to be registered with ODK.
 | `bulk_ntr_workflow/outputs/template_groups_initial.tsv` | Groups working copy (EC directives) |
 | `src/templates/<name>.template.tsv` | Final leaf template; updated in-place by Stage 4 |
 | `src/templates/<name>-groups.template.tsv` | Final groups template (equivalent class definitions) |
-| `src/templates/<name>-reports/input.tsv` | Filtered input rows + `term_type` classification |
-| `src/templates/<name>-reports/errors.tsv` | Input errors (bad/FMA/ASCTB-TEMP parents) |
-| `src/templates/<name>-reports/candidates.tsv` | Pre-mapped + OLS4-confirmed existing terms |
-| `src/templates/<name>-reports/out_of_scope.tsv` | Pathological/dysfunctional terms |
-| `src/templates/<name>-reports/name_corrections.tsv` | Source-label → corrected-label rewrites |
-| `src/templates/<name>-reports/manual_curation.tsv` | Group terms not fitting simple `part_of` pattern |
+| `bulk_ntr_workflow/outputs/<name>-reports/input.tsv` | Filtered input rows + `term_type` classification |
+| `bulk_ntr_workflow/outputs/<name>-reports/errors.tsv` | Input errors (bad/FMA/ASCTB-TEMP parents) |
+| `bulk_ntr_workflow/outputs/<name>-reports/candidates.tsv` | Pre-mapped + OLS4-confirmed existing terms |
+| `bulk_ntr_workflow/outputs/<name>-reports/out_of_scope.tsv` | Pathological/dysfunctional terms |
+| `bulk_ntr_workflow/outputs/<name>-reports/name_corrections.tsv` | Source-label → corrected-label rewrites |
+| `bulk_ntr_workflow/outputs/<name>-reports/manual_curation.tsv` | Group terms not fitting simple `part_of` pattern |
 | `bulk_ntr_workflow/outputs/definitions/input/*.json` | Per-group input for subagents |
 | `bulk_ntr_workflow/outputs/definitions/*.json` | Per-group subagent output |
 
@@ -206,13 +206,42 @@ After QC, both templates need to be registered with ODK.
 | def_xref | >A oboInOwl:hasDbXref SPLIT=\| | References + ASCTB-TEMP IRI |
 | is_a | SC % | Genus class (structural type or classification parent) |
 | part_of | SC BFO:0000050 some % | Containing structure |
+| develops_from | SC RO:0002202 some % | Optional. Developmental precursor (stage series) |
 | In_subset | AI oboInOwl:inSubset | `added_by_HRA` subset IRI |
 | Date | AT dcterms:date^^xsd:dateTime | ISO timestamp |
 | Contributor | AI dcterms:contributor | ORCID IRI |
 | Present_in_taxon | AI RO:0002175 | NCBITaxon IRI |
 | Wikipedia_image | A foaf:depiction | Wikipedia image URL |
 | xref | A oboInOwl:hasDbXref SPLIT=\| | Direct term xrefs: Wikipedia article + FMA ID |
 
+### Muscle leaf template (`<name>-muscle.template.tsv`) — Phase 7 overlay
+
+Used automatically when the source `tables` value is `muscular-system`. Adds three
+columns between `develops_from` and `In_subset`:
+
+| Header | ROBOT directive | Notes |
+|---|---|---|
+| has_muscle_origin | SC RO:0002372 some % | Bone/structure the muscle arises from |
+| has_muscle_insertion | SC RO:0002373 some % | Bone/structure the muscle inserts onto |
+| innervated_by | SC RO:0002005 some % | Motor nerve |
+
+All three are OPTIONAL — empty cell ⇒ no axiom. Populate only when Wikipedia +
+UBERON precedent provide a resolvable UBERON ID for the related entity.
+
+### Template variants and partitioning
+
+Stage 1 partitions input rows by source `tables` column → system overlay map:
+
+| Source table value | Overlay | Output template |
+|---|---|---|
+| `muscular-system` | `muscle` | `<name>-muscle.template.tsv` |
+| (anything else) | `default` | `<name>.template.tsv` |
+
+A single Stage 1 run can produce multiple leaf templates if the input has rows from
+mixed tables (each system gets its own clean template — no muscle-specific empty
+columns appear in non-muscle templates). The routing decision is printed at the start
+of Stage 1 as `Step 0 routing: muscle=N, default=M, group=K`.
+
 ### Groups template (`<name>-groups.template.tsv`) — equivalent class
 
 Same as leaf, with `is_a` / `part_of` replaced by `genus` / `location`: