CultureBotAI

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

Use this skill to manage MediaIngredientMech record identifiers. In MIM the record `identifier` IS the ontology mapping CURIE (CHEBI / FOODON / cas / kgmicrobe.compound / kgmicrobe.ingredient / mesh / NCIT / MICRO / ENVO) for a mapped ingredient, or an `UNMAPPED_NNNN` placeholder for an unmapped one — there is no separate sequential id. Use when adding or importing ingredient records, minting the next `UNMAPPED_NNNN` placeholder, promoting an unmapped record to its resolved CURIE, or reconciling identifier collisions. (Sequential `RepoName:NNNNNN` ids are a sister-repo scheme — see the cross-repo reference.)

Use this skill to deduplicate and merge MediaIngredientMech ingredient records — when two or more records describe the same ingredient (duplicate CHEBI mappings, name variants, or a placeholder plus its resolved record) and must be consolidated into one, preserving synonyms, occurrence statistics, and curation_history. Covers detection strategies, the merge procedure, and post-merge validation.

Use this skill to map MediaIngredientMech growth-media ingredient names to ontology terms (CHEBI for chemicals, FOODON for biologicals, ENVO for environmental) via exact → normalized → fuzzy → manual matching, with chemical normalization (hydrates, formulas, catalog codes) and synonym preservation. Use when curating unmapped ingredients, adding new ones, or validating existing mappings.

Use this skill to quality-check ontology-mapped MediaIngredientMech ingredient records — verify CHEBI/FOODON/ENVO terms exist and labels match (OAK), enrich chemical properties and synonyms (OLS/OWL), and catch dual-identifier, purity-merge, and kg-microbe-dictionary disagreements. Use after a curation batch, before a KG export, or for periodic maintenance. Issues are graded P1 (blocking) → P4 (optional); P3/P4 can be auto-corrected.

Validate that every ontology ID carries its correct ontology LABEL across MIM data inputs, intermediates, and data products (SSSOM/CSV). Uses LinkML schema bindings + linkml-term-validator for YAML data (canonical label) and a shared OAK validator for products (canonical-or-synonym). Run report-then-enforce; triage drift as wrong-label vs wrong-id.

Run Edison Scientific deep research (PaperQA3) for a MediaIngredientMech ingredient record to gather source-backed identity, composition, CAS-RN, and ontology-grounding (CHEBI/FOODON/NCIT) evidence. Captures a full provenance bundle and produces a curation-focused report for a curator to review and apply.

Find gaps between MIM's LinkML schema, its YAML instances, and the code that generates them. Uses linkml-validate (or the strict closed-schema harness ported from CultureMech) as ground truth and reports along three axes (schema / instances / process). Copy-paste runnable.

Use FutureHouse Falcon deep research for source-backed MediaIngredientMech ingredient curation, ontology mapping review, SSSOM predicate decisions, validation, and generated sharing artifacts.

Generate a ROBOT-template METPO proposal that lifts TraitMech synthetic traits, causal-graph scaffolding, and schema-side controlled vocabularies into METPO classes and predicates. Use when a curator-minted `traitmech:NNNNNN` ID needs a METPO home, when a causal predicate (`CausalEdge.predicate_id`) has no upstream IRI, or when a TraitMech schema enum should become first-class METPO vocabulary.

Systematic gap-and-inconsistency audit for the TraitMech LinkML schema, the trait YAML corpus, and the scripts that generate them — produces a re-runnable validation harness, schema + writer audits, and a prioritized fix backlog. Invoke when you suspect schema drift, when records are silently failing validation, after a new seeder/migration pass, or whenever the user asks to "audit the schema", "find data quality issues", or similar.

TraitMech identifier policy and workflow — METPO-first by default, with a reserved `traitmech:NNNNNN` prefix for synthetic traits that aren't in METPO. Covers looking up the right ID, minting a fallback when needed, and validating ID hygiene across the corpus.

Find gaps between TraitMech's LinkML schema, its METPO-seeded trait YAMLs, and the seeder/causal-graph scripts that write them. Uses linkml-validate as ground truth and reports along three axes (schema / instances / process). Copy-paste runnable.