X-Mech Suite: eight knowledge bases, one standard
The X-Mech suite is a fleet of eight curated, ontology-grounded knowledge bases that together describe a microbe at every scale: the habitat it lives in, the community it belongs to, the traits it expresses, the structures and proteins that implement them, the antibiotics that act on it, and the ingredients and media it is grown in. Each Mech follows the same curation model, one validated YAML record per entity with evidence and provenance, and the fleet is coordinated by a single orchestrator, culturebotai-claw.
The eight Mechs
Each card carries its Mech’s own site color. Hover a card to trace its ties in the graph above; use “Show in graph” to select it.
HabitatMech
HabitatFour habitat vocabularies harmonized into ENVO-grounded records that keep every source's attestation.
CommunityMech
CommunityCurated knowledge base of microbial communities, their interactions, cultivation conditions and evidence.
TraitMech
TraitsMicrobial ecophysiological trait knowledge base seeded from METPO, one curated YAML per trait, with causal mechanism graphs.
CellStructureMech
Cell structuresOrganelles, envelope layers, appendages, microcompartments and complexes: components, distribution, function and causal mechanism.
ProteinTraitsMech
ProteinsProtein sequence, structure and function trait classes seeded from InterPro, Pfam, Rhea, CATH, SCOPe, CARD and more.
AntibioticMech
AntibioticsOne record per antimicrobial chemical structure, harmonizing ChEBI and CARD with targets, mode of action, resistance and evidence.
MediaIngredientMech
IngredientsLLM-assisted curation of media-ingredient ontology mappings with full audit trails; owns ingredient identity for the fleet.
CultureMech
MediaVersioned, ontology-grounded knowledge base of culture-media recipes from MediaDive, TogoMedium, KOMODO and the major collections.
Shared vocabulary
The Mechs are joinable because they ground records in the same public ontologies. The table counts identifier occurrences per vocabulary in each Mech’s record corpus; darker cells mean more. Click a column to filter the graph to that vocabulary.
Counts are prefix occurrences in the canonical record directories (merged recipes for CultureMech, communities for CommunityMech, habitat records for HabitatMech) as of September 2026. ChEBI binds the chemistry arm (media, ingredients, antibiotics, proteins); NCBITaxon and ENVO bind the organism arm (habitat, community, traits); GO and METPO bridge phenotype, structure and protein.
How the Mechs reference each other
Beyond shared vocabulary, Mechs name one another directly, in record fields, in schema slots, and in the curation practices they adopt from each other. Arrows point at the Mech that consumes.
CultureMechReference class.Record data · claw ingredient_curation_pipelineculturemech_id links.Record data · docs/cross_repo_linking.mdRelatedIngredient.mediaingredientmech_id slot is declared for MIM ingredient ids; no record populates it yet.Schema slot · docs/cross_repo_linking.mddownload.yaml source catalogue, and a drift audit keeps the trait tokens the two share aligned in meaning.Practice · TraitMech download.yamlOrchestration: culturebotai-claw
culturebotai-claw is the fleet’s coordinator. It does not hold science of its own; it holds the definition of the fleet, the artifacts every Mech must share byte-for-byte, and the cross-repository pipelines that move curation between Mechs safely.
Fleet manifest
fleet.yaml is the single source of truth for which repositories form the fleet. Seven Mechs are members today; HabitatMech follows the standard and is not yet a manifest member. Every member declares every capability exactly once as enabled, disabled or not applicable, with a reason, so nothing is silently off.
Vendored governance
Shared LinkML modules (mech_shared.yaml, history.yaml), validators and behavioral contracts live in claw and are vendored into each Mech byte-identically, pinned to one immutable claw commit and checked in CI. Fifteen artifacts, all seven members.
Pipelines and skills
Three cross-repository pipelines (ingredient curation, unified ingredient mapping, ENVO environment curation) and 24 agent skills. Cross-repo writes resolve exact worktree roots, take a repository lock, default to dry run and validate staged output before replacing source data.
Which fleet contracts each member has adopted, from the manifest:
| Mech | Curation history | Strict validation | Vendored sync | Deep research | Knowledge-gap scan | Environment coverage | SSSOM export | KGX export | Source queue | Source catalogue | Site contract |
|---|---|---|---|---|---|---|---|---|---|---|---|
| CultureMech | |||||||||||
| MediaIngredientMech | |||||||||||
| CommunityMech | |||||||||||
| TraitMech | |||||||||||
| ProteinTraitsMech | |||||||||||
| AntibioticMech | |||||||||||
| CellStructureMech | |||||||||||
| HabitatMech | not yet a manifest member; vendors mech_shared.yaml without a pinned claw revision | ||||||||||
What makes a Mech
The suite is cohesive because every Mech is built the same way. The fleet standard, documented in claw’s MECH_STANDARD.md, asks for:
- One YAML record per entityA recipe, an ingredient, a community, a trait, a structure, a protein trait, an antibiotic, a habitat. The file is the unit of curation, review and history.
- A LinkML schema per MechRecords validate against the Mech's schema; every schema imports the same vendored
mech_shared.yamlfor discussions and datasets. - Ontology-grounded identityRecords are keyed by a public CURIE (ChEBI, GO, METPO, ENVO, NCBITaxon) where one exists, otherwise a minted content-hashed CURIE that can be re-grounded later.
- The ID–label invariantEvery identifier is stored with its label, and CI checks that the pair still agrees with the source ontology.
- Evidence and provenanceAssertions carry evidence items with PMIDs or DOIs; sources are catalogued with their licences before they are ingested.
- Causal mechanism graphsTraits, structures, antibiotics and habitats can carry directed, evidence-backed graphs of mechanism, sharing one node vocabulary so graphs compare across Mechs.
- Append-only curation historyEvery change is an event in a conflict-free history directory, so agents and people can curate the same corpus concurrently.
- A static browser and an open licenceEach Mech publishes a GitHub Pages browser over its records and releases under CC0-1.0 (AntibioticMech data under CC BY 4.0, CommunityMech code under BSD-3-Clause).
Related resources
- kg-microbe - The central knowledge graph the Mechs publish into and draw from
- MicroGrowAgents - Multi-agent media design built on CultureMech, MediaIngredientMech and kg-microbe
- Resources - The full tool catalogue, including MicroMediaParam and the kg-microbe utilities
- METPO - The Microbial Ecophysiological Trait and Phenotype Ontology that seeds TraitMech and grounds trait references across the fleet
Bibliography
- 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;giag077. 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
See the full bibliography on the Publications page.