What is a Mech?

A Mech is a knowledge base built on a specific pattern. The pattern was set by DisMech and is followed by the microbial Mechs of the X-Mech suite. The name comes from mechanism: the first Mechs record how something works, not just that it exists.

The pattern has these parts.

One record per entity. A disorder, a habitat, a community, a trait, a structure, a protein trait class, a natural product, an antibiotic, an ingredient, a recipe. Each is one YAML file. The file is the unit of curation, review and history.

A LinkML schema. Records validate against the Mech’s own schema, with closed validation, on every change. The X-Mech suite schemas also import a shared module, mech_shared.yaml, ported from DisMech, that supplies Discussion (open questions, knowledge gaps, controversies, curation to-dos) and Dataset classes.

Ontology-grounded identity. Records are keyed by a public CURIE where one exists: ChEBI, GO, METPO, ENVO, NCBITaxon, Mondo. Where none does, the Mech mints a content-hashed CURIE in its own namespace that can be re-grounded later. Every identifier is stored with its label, and CI checks that the pair still agrees with the source ontology.

Evidence and provenance. Claims carry evidence items with PMIDs or DOIs. In DisMech every evidence item quotes the cited abstract verbatim and a validator fetches the abstract and checks the quote. Sources are catalogued with their licenses before they are ingested.

Causal mechanism graphs. Disorders, traits, structures, antibiotics and habitats can carry directed, evidence-backed graphs of mechanism. The X-Mech suite shares one node vocabulary so that graphs compare across Mechs.

Append-only curation history. Every change is an event in a history directory that only grows, so agents and people can curate the same corpus at the same time without conflicts.

AI agents write most of it. People review it. Content is generated and maintained by AI curation agents. The human gate is the pull request. Automated validation guarantees that citations exist, quotes are exact and ontology terms are real. It does not guarantee that the science is right, and the Mechs say so.

A static browser and an open license. Each Mech publishes a site over its records and releases them under CC0 or CC BY.

What a Mech is not

A Mech is not a knowledge graph, though several export to KGX and feed KG-Microbe. A knowledge graph flattens records into nodes and edges. A Mech keeps the record, with its evidence, its history and its open questions, as the thing that is curated. For knowledge graphs, see KG-Registry.

A Mech is not an ontology. It grounds in ontologies and asks them for terms it lacks.

The fleet standard

The X-Mech suite maintains a written standard, MECH_STANDARD.md, derived by measuring the established Mechs. It names what a repository must hold to be a Mech, what it may reuse, and what is nobody’s business but its own. The fleet is coordinated by culturebotai-claw, which holds the fleet manifest, the vendored shared artifacts and the cross-repository pipelines.