TraitMech
traitmech
active reviewed x-mech-suitekg-microbe
TraitMech is a knowledge base of microbial ecophysiological traits, seeded from METPO, the Microbial Ecophysiological Trait and Phenotype Ontology, and curated incrementally. Each trait, such as Gram type, motility, pH optimum or halophily, lives in its own YAML file with provenance back to its METPO source class and, where curated, literature evidence and a causal mechanism graph. Chemicals, microbes and enzymes are not seeded here. They belong to MediaIngredientMech and CultureMech.
One record is
a microbial ecophysiological trait
1105 records as of 2026-10-12
Counted from data/traits/*.yaml at a57b006. 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 CausalEdge carries at least one EvidenceItem with a PMID or DOI. Records carry a curation status of SEEDED, PROPOSED, REVIEWED or DEPRECATED. |
| Validation in CI | schema ontology_terms references |
| Append-only history | Yes |
| Record identifiers | Records are keyed by their METPO CURIE. |
Features
- causal_mechanism_graphs Records carry directed, evidence-backed graphs of mechanism.
- 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.
Grounding and sources
Ontologies and vocabularies: METPO GO NCBITaxon CHEBI UniProt PATO
| Source | Relation | What is taken |
|---|---|---|
| METPO | prov:wasDerivedFrom | The seed. Every trait record traces to a METPO class (METPO 2025-11-25). |
| PubMed | prov:used | Evidence on causal graph edges. |
Products
| Product | Kind | Format | Description |
|---|---|---|---|
Trait recordstraitmech.records |
RecordCorpus | yaml | One YAML file per trait under data/traits/ |
TraitMech LinkML schematraitmech.schema |
DataModelProduct | linkml
linkml mech_shared |
|
TraitMech browsertraitmech.browser |
GraphicalInterface | html |
Relations to other Mechs
- follows_pattern_of dismech
- adopts_practice_of proteintraitsmech: TraitMech adopted ProteinTraitsMech's licence-bearing download.yaml source catalogue, and a drift audit keeps shared trait tokens aligned.
- hands_off_to mediaingredientmech: Chemicals are not seeded in TraitMech.
- hands_off_to culturemech: Growth media are not seeded in TraitMech.
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.
Of 491 record files, 427 are REVIEWED, 50 DEPRECATED and 14 PROPOSED as of the README on 2026-09-10. 353 reviewed records carry causal graphs.