Add single-record YAML curation skill

.claude/skills/curate-yaml-record/SKILL.md

@@ -0,0 +1,133 @@
+---
+name: curate-yaml-record
+description: Review and curate one CellStructureMech structure YAML record for structure identity, hierarchy and parthood, composition, taxonomic scope, function, evidence, completeness, and resolvable gaps. Use for a named record audit or improvement; do not use for bulk source ingestion, generated page edits, or as permission to spend credits, contact anyone, or mutate GitHub.
+allowed-tools: Bash, Read, Grep, Glob, WebSearch, WebFetch, Edit, Write
+metadata:
+  category: curation
+  requires_database: false
+  requires_internet: true
+  version: 1.0.0
+---
+
+# Curate one CellStructureMech YAML record
+
+Produce a defensible `CellStructureRecord` and an explicit account of what is
+supported, corrected, unresolved, and genuinely unknown. Search results and
+research reports are leads; only inspected sources can support a claim.
+
+## Boundaries
+
+- Resolve one target under `data/structures/<category>/`. Stop and disambiguate
+  when a label could denote a structure, component protein, phenotype, broader
+  system, or specific multi-protein complex.
+- Review/audit requests are read-only. Curate, improve, complete, correct, or
+  add-evidence requests authorize local edits to the named record and the
+  smallest necessary provenance/generated paths.
+- Never edit generated `pages/`; edit the record or template and regenerate.
+- Never launch paid research, contact anyone, or create/edit a GitHub item or
+  outbound message without explicit authorization.
+- Preserve unrelated work and use a dedicated branch/worktree.
+- Never fill an optional field for coverage or infer false from absence.
+
+## Read before judging the record
+
+Read the full target plus:
+
+- `CLAUDE.md`, `docs/CURATION.md`, and `docs/SCHEMA.md`;
+- relevant `CellStructureRecord`, component, composition, function, taxonomic,
+  image, evidence, causal-graph, discussion, and history classes in
+  `src/cellstructuremech/schema/cellstructuremech.yaml`;
+- `history/README.md` and the source-queue entry when relevant;
+- [references/review-checklist.md](references/review-checklist.md).
+
+Inspect parent/part records, linked TraitMech records, source-native ontology or
+database records, and cited literature. Rendered pages and raw research notes
+are not independent evidence.
+
+## Workflow
+
+### 1. Establish the baseline
+
+Read the whole YAML. Record identifier, definition/source, category/kind,
+parents, parthood, components/compositions, taxa, examples, functions, linked
+traits, properties, images, evidence, graphs, discussions, datasets, status,
+and history. Run:
+
+```bash
+just validate <record-path>
+just validate-strict <record-path>
+```
+
+Use `just validate-products` and `just check-trait-links --check` when the
+record's ontology and trait links are in scope. A green schema gate proves
+shape, not biological correctness.
+
+### 2. Verify structure identity and relations first
+
+A record is a microbial cell structure, not a component protein or phenotype;
+the finest supported unit is a multi-protein complex. Prefer a GO cellular-
+component CURIE only when it denotes the exact structure. Otherwise retain a
+CellStructureMech identity and use the broader term appropriately.
+
+Verify `parent_structures` as is-a and `part_of`/`has_part` as parthood. Check
+category, kind, replacements, xrefs, and canonical labels. Never guess a CURIE
+or use a broader/related term as exact identity.
+
+### 3. Review every scientific claim
+
+Verify each component and stoichiometry, taxonomic-distribution statement,
+canonical example, function, trait link, physical property, image attribution,
+dataset, and causal edge against its exact source and context. Distinguish
+source database assertions, primary experiments/imaging, reviews, predictions,
+and search snippets.
+
+Every composition item, function, taxonomic-distribution entry, image, and
+causal edge must meet the evidence rules in `docs/CURATION.md`. Do not
+generalize a protein family's presence into structure presence or one organism's
+architecture to all taxa. Snippets are short verbatim source text.
+
+### 4. Assess completeness and resolve supported gaps
+
+Apply the checklist and use bounded searches for consequential gaps. Prioritize:
+
+1. wrong structure identity, granularity, hierarchy, or parthood;
+2. incorrect/unsupported components or complex composition;
+3. overbroad taxonomic distribution or canonical examples;
+4. unsupported function, trait, physical-property, or causal claims;
+5. missing imaging/experimental provenance for material assertions.
+
+Do not manufacture a component, function, taxonomic absence, or mechanism.
+Add a discussion only for a concrete conflict or consequential curation task.
+
+### 5. Write through the guarded path
+
+Use a narrowly scoped mutator that asserts the target ID/path, calls
+`cellstructuremech.curate.curation_event.record_curation_event` with
+`llm_assisted=True`, and writes through
+`cellstructuremech.validation.write_validated.write_validated_structure`.
+Use `curator="claude"` when no curator identity was supplied; never attribute
+agent judgement to the user.
+
+Create an append-only repository history record with `just new-history`. Do not
+add either event when content is unchanged. An LLM-authored record remains
+`mapping_status: PROPOSED`; only a human curator may mark it REVIEWED.
+
+### 6. Verify and report
+
+```bash
+just validate-strict <record-path>
+just validate-history
+just validate-products
+just check-trait-links --check
+just qc
+git diff --check
+git diff -- <record-path> history src scripts pages
+```
+
+If a record changed, run `just render` and include the checked generated output
+when repository policy requires it. Re-read the YAML and confirm citations,
+status, path/category, and both histories match the actual diff.
+
+Report corrections/additions and sources, retained claims checked, unresolved
+gaps and bounded searches, mapping status and human sign-off state, history
+artifact, and all validation results.

.claude/skills/curate-yaml-record/references/review-checklist.md

@@ -0,0 +1,29 @@
+# CellStructureRecord review checklist
+
+Use this checklist for one microbial cell structure. It is not a requirement
+to populate every optional slot or invent a causal graph.
+
+## Evidence standard
+
+- Put evidence on the narrowest component, composition, taxonomic, function,
+  image, property, or causal assertion it supports.
+- Verify stable IDs and inspect source-native records or source text.
+- A protein annotation, predicted structure, or sequence hit does not alone
+  establish assembly, localization, function, or taxonomic distribution.
+- Snippets are short exact text; interpretation belongs in notes.
+- Preserve conflicts and bounded “not found” results as uncertainty.
+
+## Field-by-field audit
+
+| Area | Verify | Complete enough when |
+|---|---|---|
+| Identity | ID, label, definition/source, category, and kind denote one structure or complex. | Protein, phenotype, broader system, and structure boundaries are explicit. |
+| Hierarchy/parthood | Parents are is-a; `part_of` and `has_part` are real mereological relations. | Related structures are not forced into hierarchy or identity. |
+| Components | Protein/family identity, role, stoichiometry, evidence, and source version agree. | Membership is distinguished from necessary composition and variable accessory parts. |
+| Complex composition | Subcomplexes, counts, assembly context, and organism/condition scope agree. | A model from one species is not silently universalized. |
+| Taxonomic distribution | Taxon/strain, presence/absence wording, method, and evidence agree. | Absence is asserted only from evidence capable of detecting the structure. |
+| Functions/traits | Function, trait link, direction, organism/context, and evidence agree. | Association is not upgraded to mechanism or exclusivity. |
+| Properties/images | Measurement, units, method, figure/repository accession, attribution, and license agree. | Visuals and values are traceable to the exact structure/context. |
+| Causal graph | Scope, nodes, edges, direction, and edge-level evidence agree. | Every edge is supported and predictions remain labeled. |
+| Discussions/datasets | Each item is relevant, durable, and actionable. | No placeholder or bibliography dump remains. |
+| Status/audit | Mapping status and both history surfaces match the review performed. | Agent drafts stay PROPOSED; REVIEWED has human sign-off. |

CLAUDE.md

@@ -21,6 +21,10 @@ Read before changing domain content:
 - Issue triage: the `review-open-issues` skill
   (`.claude/skills/review-open-issues/SKILL.md`) — read-only ranking of the
   whole queue; closing and merging stay the owner's calls.
+- Single-record review and evidence-backed improvement: the
+  `curate-yaml-record` skill
+  (`.claude/skills/curate-yaml-record/SKILL.md`). Audit requests are read-only;
+  mutation requires an explicit curation request and the guarded writer.
 
 Sibling repositories use the same conventions: TraitMech, ProteinTraitsMech,
 HabitatMech, CultureMech, MediaIngredientMech, CommunityMech. The upstream