NaturalProductMech
naturalproductmech
active seeded x-mech-suite
NaturalProductMech is a knowledge base of individual natural product structures. One record is one chemical structure made by a living organism, carrying who makes it, from which biosynthetic gene cluster, what it does, and the evidence for all three. MIBiG, ChEBI, LOTUS, CyanoMetDB, NPClassifier, PubChem BioAssay and BindingDB are harmonized onto one record per InChIKey. Every record is currently SEEDED. The biosynthetic pathway and causal graph fields are empty and are the work the rest exists for.
One record is
a natural product chemical structure
3115 records as of 2026-10-12
Counted from data/natural_products/*.yaml at e66f934. 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 |
| Evidence policy | Producer organisms carry biosynthesis-grade evidence. Occurrences are cited. The corpus reproduces offline from committed inventories. |
| Validation in CI | schema ontology_terms 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: naturalproductmech. |
Features
- 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.
Grounding and sources
Ontologies and vocabularies: CHEBI NCBITaxon MIBiG NPAtlas PubChem UniProt
| Source | Relation | What is taken |
|---|---|---|
| MIBiG | prov:hadPrimarySource | Structures, producer organisms and biosynthetic gene clusters. |
| ChEBI | prov:hadPrimarySource | Grounding and biological origins. |
| LOTUS | prov:hadPrimarySource | Cited occurrences. |
| CyanoMetDB | prov:hadPrimarySource | Cited occurrences for cyanobacterial metabolites. |
| NCBI Taxonomy | prov:used | Name resolution for producers. |
| NPClassifier | prov:used | The filing pathway for each structure. |
| PubChem BioAssay | prov:used | Measured activities and targets. |
| BindingDB | prov:used | Measured activities and targets. |
Products
| Product | Kind | Format | Description |
|---|---|---|---|
Natural product recordsnaturalproductmech.records |
RecordCorpus | yaml | One YAML file per structure under data/natural_products/ |
NaturalProductMech LinkML schemanaturalproductmech.schema |
DataModelProduct | linkml
linkml mech_shared |
Relations to other Mechs
- follows_pattern_of dismech
- consumes antibioticmech: Antimicrobial classification and cross-corpus links come from AntibioticMech.
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.
Not yet declared in the X-Mech fleet manifest as of 2026-09-10. It vendors the governed artifacts one revision behind the other eight.