HabitatMech
habitatmech
active curating x-mech-suitekg-microbe
HabitatMech is a knowledge base of microbial habitats and environments. Four source vocabularies that describe where microbes are found, JGI GOLD ecosystem paths, BacDive isolation sources, PREGO ontology annotations and the Madin et al. literature curation, are harmonized into records grounded in ENVO, UBERON, FOODON and BTO. Each source term becomes a source concept, each concept resolves to an identifier, and concepts that resolve to the same identifier merge into one record that keeps every source’s attestation.
One record is
a microbial habitat or environment
3208 records as of 2026-10-12
Counted from data/habitats/*.yaml at 679a57e. 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 | Records keep each source's attestation and assertion volume. Causal graphs carry evidence items with PMIDs or DOIs on every edge. |
| Validation in CI | schema ontology_terms references corpus_reproduction |
| Append-only history | Yes |
| Record identifiers | An ontology CURIE where one is defensible, otherwise a minted, content-hashed CURIE that can be re-grounded later. Minted prefix: habitatmech. |
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: ENVO UBERON FOODON BTO NCBITaxon
| Source | Relation | What is taken |
|---|---|---|
| JGI GOLD | prov:hadPrimarySource | Five-level ecosystem classification paths. |
| BacDive | prov:hadPrimarySource | Flat isolation-source labels. |
| PREGO | prov:hadPrimarySource | ENVO-annotated organism-environment associations. |
| Madin et al. trait database | prov:hadPrimarySource | Literature-curated habitat assignments. |
| KG-Microbe | prov:used | Environmental parameters attached to records. |
Products
| Product | Kind | Format | Description |
|---|---|---|---|
Habitat recordshabitatmech.records |
RecordCorpus | yaml | One YAML file per habitat, filed by category (host-associated, engineered, aquatic, terrestrial, food, air, clinical, other). |
HabitatMech LinkML schemahabitatmech.schema |
DataModelProduct | linkml
linkml mech_shared |
|
HabitatMech browserhabitatmech.browser |
GraphicalInterface | html | Every record by category, plus the ENVO term requests the project is asking the ontology community for. |
Relations to other Mechs
- follows_pattern_of dismech
- shares_vocabulary_with traitmech: Habitat causal graphs use a superset of TraitMech's node vocabulary, so a node may be a TraitMech or METPO trait.
- hands_off_to culturemech: The one overlapping concept, BTO:0000316 culture medium, is handed to CultureMech rather than curated twice.
Referenced by
Contacts
- CultureBotAI (Organization) CultureBotAI https://culturebotai.github.io/
- 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.
Joined the X-Mech fleet manifest on 2026-09-07.