CommunityMech
communitymech
active curating x-mech-suitekg-microbe
Also known as: Microbial Community Mechanisms Knowledge Base
CommunityMech is a knowledge base of microbial communities: their composition, ecological interactions, cultivation conditions, environments and supporting evidence. Curated YAML is the canonical record format. Validation, the static browser and the KGX export are all derived from it. Community records name the culture medium they were cultivated in by CultureMech identifier. The project is adapted from DisMech.
One record is
a microbial community
458 records as of 2026-10-12
Counted from kb/communities/*.yaml at 80049bc. Refreshed weekly.
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 | Interactions and cultivation claims carry evidence items with references. Cached source text in the repository makes evidence checks reproducible offline. |
| Validation in CI | schema ontology_terms references cross_field |
| Append-only history | Yes |
Features
- evidence_snippets Evidence items quote the cited source verbatim.
- 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.
- kgx_export Records export to KGX nodes and edges.
Grounding and sources
Ontologies and vocabularies: NCBITaxon CHEBI GO ENVO GTDB
| Source | Relation | What is taken |
|---|---|---|
| PubMed | prov:hadPrimarySource | Literature evidence for community composition and interactions, cached in references_cache for reproducible checks. |
| GTDB | prov:used | Taxonomy for community members. |
Products
| Product | Kind | Format | Description |
|---|---|---|---|
Community recordscommunitymech.records |
RecordCorpus | yaml | Canonical MicrobialCommunity records in kb/communities, with reusable CommonTaxon records in kb/taxa. |
CommunityMech LinkML schemacommunitymech.schema |
DataModelProduct | linkml
linkml mech_shared |
|
KGX exportcommunitymech.kgx |
GraphProduct | kgx
kgx biolink |
Nodes and edges emitted by a deterministic Python emitter from the community YAML. |
CommunityMech browsercommunitymech.browser |
GraphicalInterface | html |
Relations to other Mechs
- follows_pattern_of dismech
- consumes culturemech: Community records name the medium they were cultivated in by CultureMech id.
- consumes mediaingredientmech: The RelatedIngredient.mediaingredientmech_id slot is declared for MediaIngredientMech ingredient ids. No record populates it yet.
Referenced by
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.