AntibioticMech
antibioticmech
active curating x-mech-suitekg-microbe
AntibioticMech is a knowledge base of individual chemical structures with antimicrobial activity, harmonized from ChEBI and CARD’s Antibiotic Resistance Ontology. One record is one chemical structure, keyed by its ChEBI identifier and carrying SMILES, InChI and InChIKey. A class such as macrolide antibiotic is not a record. It is a structural_class on the records it covers. Each record carries what the compound hits, how microbes resist it, and the evidence for both.
One record is
an antimicrobial chemical structure
2939 records as of 2026-10-12
Counted from data/antibiotics/*.yaml at 0611c4e. 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 | Targets and resistance determinants carry evidence. Candidate sources are ranked in a source queue and their licences verified and recorded before ingestion. |
| Validation in CI | schema ontology_terms references corpus_reproduction |
| Append-only history | Yes |
| Record identifiers | A ChEBI CURIE where the entry has a structure, otherwise a minted, content-hashed CURIE. A record with no InChIKey is never written. Minted prefix: antibioticmech. |
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: CHEBI ARO CAS PubChem DrugBank NCBITaxon
| Source | Relation | What is taken |
|---|---|---|
| ChEBI | prov:hadPrimarySource | Structures, definitions and antimicrobial class terms. |
| CARD | prov:hadPrimarySource | Antibiotic Resistance Ontology classification, molecular targets and resistance determinants. |
| PubChem | prov:used | The structures CARD's cross-references point at. |
Products
| Product | Kind | Format | Description |
|---|---|---|---|
Antibiotic recordsantibioticmech.records |
RecordCorpus | yaml | One YAML file per structure under data/antibiotics/ |
AntibioticMech LinkML schemaantibioticmech.schema |
DataModelProduct | linkml
linkml mech_shared |
|
AntibioticMech browserantibioticmech.browser |
GraphicalInterface | html | Every record by antimicrobial class, with structures, sources, CARD targets and resistance determinants. |
Relations to other Mechs
- follows_pattern_of dismech
- provides_to naturalproductmech: Supplies antimicrobial classification and cross-corpus links.
- provides_to cellstructuremech: Wrote the licensed source-queue pattern that CellStructureMech adapted.
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.