CultureMech
culturemech
active curating x-mech-suitekg-microbe
Also known as: Microbial Culture Media Knowledge Graph
CultureMech is a versioned knowledge base of microbial culture-media recipes from MediaDive, TogoMedium, KOMODO and the major culture collections. It combines LinkML validation, ontology grounding, provenance, deduplication, browser exports and static recipe pages. The corpus has four layers: immutable raw source payloads, mechanical source-shaped YAML, authoritative normalized records that preserve source-specific formulations, and reproducible merged records that are the deduplicated canonical output. The merged layer is what this entry counts.
One record is
a culture-medium recipe
6320 records as of 2026-10-12
Counted from data/merge_yaml/merged/*.yaml at 9976e05. Refreshed weekly.
License
Records: CC0 1.0
Curation model
| Agent-curated | Yes. AI agents generate or maintain most of the content. |
|---|---|
| Human review | pull_request. Agent changes arrive as pull requests that a person reviews and merges. |
| Agents and tools | Claude Code, culturebotai-claw |
| Evidence policy | Every recipe keeps its source provenance. Normalized records preserve source-specific formulations and merged records record which normalized records they combine. |
| Validation in CI | schema ontology_terms cross_field corpus_reproduction |
| Append-only history | Yes |
Features
- ontology_grounding Entities bind to public ontology terms with labels.
- append_only_history Every change is an event in an append-only history directory.
- knowledge_gaps Records carry structured open questions, controversies and curation to-dos.
- static_browser A static site lets a reader browse every record.
- sssom_export Mappings export as SSSOM.
Grounding and sources
Ontologies and vocabularies: CHEBI KEGG FOODON UBERON CAS NCBITaxon
| Source | Relation | What is taken |
|---|---|---|
| MediaDive | prov:hadPrimarySource | DSMZ culture-media recipes and solution volumes. |
| TogoMedium | prov:hadPrimarySource | |
| KOMODO | prov:hadPrimarySource | Recipes and base volumes. |
| MediaIngredientMech | prov:used | Curated ingredient identity and ontology mappings synced back into recipes. |
Products
| Product | Kind | Format | Description |
|---|---|---|---|
Merged recipe recordsculturemech.records |
RecordCorpus | yaml | Reproducible, deduplicated canonical recipes. The normalized layer holds 15,878 source-specific records behind them. |
Normalized recipe recordsculturemech.normalized |
RecordCorpus | yaml | Authoritative curated and validated records, one per source formulation. |
CultureMech LinkML schemaculturemech.schema |
DataModelProduct | linkml
linkml mech_shared |
|
CultureMech browserculturemech.browser |
GraphicalInterface | html | Browser-based exploration and static recipe pages. |
Relations to other Mechs
- follows_pattern_of dismech
- provides_to mediaingredientmech: Unmapped ingredient strings and occurrence counts become MediaIngredientMech's curation backlog.
- consumes mediaingredientmech: Vendors MediaIngredientMech's ingredient-role enums and consumes its immutable label index.
- provides_to communitymech: Community records cite the medium they were cultivated in by CultureMech id.
Referenced by
Publications
- Santangelo BE, Hegde H, Caufield JH, Reese J, Kliegr T, Hunter LE, Lozupone CA, Mungall CJ, Joachimiak MP. KG-Microbe: Building Modular and Scalable Knowledge Graphs for Microbiome and Microbial Sciences. GigaScience. 2026. doi:10.1093/gigascience/giag077
- Naseem S, Miller MA, Martinez-Gomez NC, Sun N, Joachimiak MP. MicroGrowAgents: An Agentic AI System for Microbial Cultivation Engineering. bioRxiv. 2026. doi:10.64898/2026.06.04.729985
Contacts
- CultureBotAI (Organization) CultureBotAI
- Marcin P. Joachimiak (Individual) ORCID 0000-0001-8175-045X mjoachimiak@lbl.gov realmarcin
Registry entry
Created 2026-09-10. Last modified 2026-09-10. Edit this entry on GitHub.
The two publications describe KG-Microbe and MicroGrowAgents, which CultureMech feeds. Neither is a CultureMech paper.