CellStructureMech
cellstructuremech
active curating x-mech-suitekg-microbe
CellStructureMech is a knowledge base of microbial cell structures: organelles, envelope layers, appendages, microcompartments, inclusions, cytoskeletal systems and the multi-protein complexes that build them. One record is a structure you could point to in a micrograph, from a whole organelle down to a discrete complex such as the flagellar motor. A record holds components with stoichiometry and UniProt examples, taxonomic distribution, GO functions with evidence, the TraitMech phenotypes it confers, and causal graphs of assembly, operation and regulation with every edge cited. It fills the layer between a phenotype in TraitMech and a protein in ProteinTraitsMech.
One record is
a microbial cell structure or multi-protein complex
909 records as of 2026-10-12
Counted from data/structures/*.yaml at 937ba62. 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 causal graph edge and every function claim carries a citation. Candidate sources are ranked in a source queue and their licences verified before ingestion. |
| Validation in CI | schema ontology_terms references corpus_reproduction |
| Append-only history | Yes |
| Record identifiers | A GO cellular component CURIE where one exists, otherwise a minted 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.
- embeddings_explorer The site offers an embedding map or nearest-neighbour view of records.
Grounding and sources
Ontologies and vocabularies: GO NCBITaxon UniProt METPO Pfam PDB
| Source | Relation | What is taken |
|---|---|---|
| UniProtKB | prov:used | Taxon-paired protein examples for components. |
| PubMed | prov:hadPrimarySource | Evidence on functions and on causal graph edges. |
Products
| Product | Kind | Format | Description |
|---|---|---|---|
Structure recordscellstructuremech.records |
RecordCorpus | yaml | |
CellStructureMech LinkML schemacellstructuremech.schema |
DataModelProduct | linkml
linkml mech_shared |
|
CellStructureMech browsercellstructuremech.browser |
GraphicalInterface | html | Every record by category, with components, distribution, functions and mechanism graphs, plus a text embedding map with nearest neighbours. |
Relations to other Mechs
- follows_pattern_of dismech
- consumes traitmech: A structure lists the phenotypes it confers as TraitMech or METPO terms, and its causal-graph node vocabulary is TraitMech's plus a STRUCTURE node type.
- hands_off_to proteintraitsmech: A single protein is a component of a structure, never a record of its own. It grounds to InterPro or UniProtKB and hands off to ProteinTraitsMech.
- adopts_practice_of antibioticmech: Adapted AntibioticMech's licensed source-queue pattern.
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.
All 92 records carry the PROPOSED status as of the README on 2026-09-10.