CultureMech

Use this skill to quality-check CultureMech growth-media and solution recipes — verify schema/structure, MediaIngredientMech ingredient linkages and CHEBI mappings, solution references, data quality (placeholders, units, concentrations), and categorization. Use after creating/editing a recipe, before a KG export, or for periodic maintenance. Issues are graded P1 (blocking) → P4 (optional); P3/P4 can be auto-fixed.

Use this skill to manage CultureMech record identifiers — find the highest existing CultureMech id, mint the next id, and insert new media/solution records with correct id placement. Use when adding or importing recipe records, or reconciling id collisions.

Use this skill to integrate the MediaIngredientMech ingredient variant hierarchy (parent/child relationships — purity levels, hydrates, stereoisomers) into CultureMech recipe ingredient references. Use when linking recipe ingredients to their canonical MIM records or resolving variant forms.

Validate that every ontology ID carries its correct ontology LABEL across CultureMech recipe YAMLs and SSSOM mapping products. Uses LinkML schema bindings + linkml-term-validator for term.{id,label} (canonical label) and a shared OAK validator for products. Run report-then-enforce; triage drift as wrong-label vs wrong-id.

Scrape growth-medium recipes directly from the RIKEN JCM GRMD database and emit CultureMech-normalized YAML records. Use to close the gap between CultureMech's JCM coverage (originally ingested second-hand via MediaDive/TOGO) and the live JCM catalogue — e.g. when newly added high-GRMD media are missing, or to audit JCM completeness.

Generate an interactive UMAP scatter plot of CultureMech CHEBI ingredients in KG-Microbe embedding space — each point is one unique ingredient, sized by frequency and colored by occurrence tier

Run Edison Scientific deep research for a CultureMech medium record, then for each candidate organism returned by phase 1 run a per-organism follow-up that extracts the recipe, culture conditions, identifiers, and citation metadata from the primary publication. Produces a curation-focused report with proposed YAML changes.

Identify and populate the kg_microbe_match field for CultureMech media records by finding exact ingredient matches in the KG-Microbe mediadive graph

Systematic gap-and-inconsistency audit for the CultureMech LinkML schema, the YAML instance corpus, and the scripts that generate them — produces a re-runnable validation harness, three audit reports, and a prioritized fix backlog. Invoke when you suspect schema drift, when records are silently failing validation, when a new bulk migration has been added, or whenever the user says "audit the schema", "find data quality issues", "what's wrong with the records", "are we silently failing validation", or similar.

Lightweight linkml-validate-based check for CultureMech schema/data drift, classified along three axes (schema / instances / process). For the comprehensive audit (also scans pipeline/writers, emits TSV reports + re-runnable harness), use `audit-schema-gaps` instead.

Create new growth media or solution YAML records from input data or documents