Knowledge base of individual natural product structures — one record per chemical structure made by a living organism, carrying who makes it, from which gene cluster, what it does, and the evidence for all three.
NaturalProductMech is the biosynthetic-origin counterpart of AntibioticMech (antimicrobial compounds and their mechanisms), TraitMech (traits), CultureMech (growth media), MediaIngredientMech (ingredients), HabitatMech (habitats), CellStructureMech (cell structures), ProteinTraitsMech (proteins) and CommunityMech (communities), and follows the curation pattern established by dismech: one YAML per entity, ontology-grounded, evidence-backed, schema-validated, curated incrementally.
2026-09-09. The corpus reproduces offline from committed inventories:
MIBiG (structures, producers, gene clusters), ChEBI (grounding, origins),
LOTUS and CyanoMetDB (cited occurrences), NCBI Taxonomy (name resolution),
NPClassifier (the filing pathway), PubChem BioAssay and BindingDB (measured
activities and targets), and AntibioticMech (antimicrobial classification and
cross-corpus links). Every record remains SEEDED until a curator signs off
identity, structure, filing class, and producer claims; partial
biosynthetic_pathway and causal_graphs curation is now underway. Owed work
is in NEXT_TASKS.md.
Curated mechanisms can use inline graphs or exact-owner components referenced
by causal_graph_refs. Use the resolving reader for the complete mechanism;
see curation for the data contract.
records: 3115
unique InChIKeys: 3115
structures with undefined stereocentres: 1124
by pathway (the filing decision, computed):
ALKALOIDS 509
AMINO_ACIDS_AND_PEPTIDES 655
CARBOHYDRATES 103
FATTY_ACIDS 82
POLYKETIDES 869
SHIKIMATES_AND_PHENYLPROPANOIDS 64
TERPENOIDS 213
UNCLASSIFIED 620
by curation status:
SEEDED 3115
by grounding status:
EXACT 362
MINTED 2744
REVIEW_NEEDED 9
field coverage (records carrying at least one item):
biosynthesis_origin 3115
producer_taxon_groups 3076
occurrence_taxon_groups 2342
producer_organisms 3076
occurrences 2342
biosynthetic_gene_clusters 3115
biosynthetic_pathway 157
bioactivities 176
bioactivity_summary 317
molecular_targets 14
causal_graphs 241
related_records 209
discussions 325
producer claims: 3407 (808 causal, 162 correlational)
BGC_CHARACTERIZED 808
BGC_CORRELATED 162
SOURCE_ASSERTION 2437
cluster link claims: 3449 (1359 demonstrated)
CLUSTER_CORRELATED 110
CLUSTER_DEMONSTRATED 1359
CLUSTER_PREDICTED 2
CLUSTER_UNSTATED 1978
records where a producer taxon is independently corroborated by a cited occurrence: 732
records whose only origin evidence is a gene cluster with no named host: 27
These grade two different questions and they come apart. A producer
claim says this TAXON makes the compound; a cluster link says this
LOCUS does. Heterologous expression settles the second and leaves the
first exactly where the isolation report left it.
Development uses Python 3.13 via .python-version; CI selects the same minor
explicitly and runs the full quality gate once. The package compatibility
floor remains declared in pyproject.toml.
just install # uv sync --locked --extra dev --extra chemistry
just qc # every local and CI quality gate
just seed # dry run: what would be written, per pathway
just report # corpus, grounding and origin-evidence coverage
just source-queue # the ranked data-source queueNothing above touches the network.
| Document | What it is |
|---|---|
| PLAN.md | Scope, schema design, the AntibioticMech join, milestones M0–M6 |
| CLAUDE.md | Operational guidance for editing agents: commands, boundaries, invariants |
| NEXT_TASKS.md | Owed work, by issue, in the order it is worth doing |
| docs/HARMONIZATION.md, docs/CURATION.md | Identity, merging and scope; decision semantics and evidence rules |
| research/2026-09-07-natural-product-data-sources.md | The verified source landscape, with focused follow-up reports beside it |
| curation/source_queue.tsv | 43 sources, ranked — 9 adopted — with licence status and the gap each closes |
| .claude/skills/ | Five repo-local curation workflows |
| src/naturalproductmech/schema/ | The LinkML schema, closed-validated |
| conf/ | Scope and the record budget, the producer-evidence grading, the adopted and staged sources, the sibling pin |
AntibioticMech answers what a compound does to a microbe and how the microbe resists it. It has nowhere to say who makes erythromycin, from which gene cluster, by which pathway. TraitMech says an organism produces antibiotics; ProteinTraitsMech says what a polyketide synthase domain is. None of them says which structure a given Streptomyces strain makes, from which locus, with what evidence.
| Section of a record | Question it answers |
|---|---|
producer_organisms |
Which taxon biosynthesizes it, and how do we know? |
occurrences |
Where has it been found, and in whose paper? |
biosynthetic_gene_clusters |
Which cluster, in which genome, at which coordinates? |
biosynthetic_pathway |
Which enzymes, in which order? |
bioactivities / molecular_targets |
What does it do, measured how? |
causal_graphs |
How is it made, and how does it act? Every edge cited. |
One record is one chemical structure, keyed on a Standard InChIKey. A compound class is not a record. Neither is an extract, a fraction, an essential oil or a herbal preparation — activity measured on a mixture is not evidence about any constituent of it.
Occurrence is not production. A compound isolated from a sponge may be made
by its bacterial symbiont; one "found in" a plant extract may come from a
fungal endophyte. So producer_organisms requires biosynthesis-grade evidence
— a gene cluster with experimental support, heterologous expression, isotope
feeding, or production by an axenic culture — while occurrences requires a
cited isolation or detection report. The seeder never promotes one to the
other. That distinction is why LOTUS's 674,454 structure–organism–reference
triples are occurrences, and why MIBiG's per-locus evidence vocabulary is what
grades a producer claim.
The first release seeds from six sources whose licences were verified against their own terms pages on 2026-09-07:
| Source | Licence | Contributes |
|---|---|---|
| MIBiG 4.0 | CC BY 4.0 | producers with NCBI taxid, gene clusters, cluster class, references |
| ChEBI | CC BY 4.0 | identity, structures, specialized-metabolite roles |
| LOTUS via Wikidata | CC0 | referenced occurrences |
| NPClassifier | CC0 | the filing classification, computed from structure |
| PubChem | public domain | structures the others lack |
| CyanoMetDB | CC BY 4.0 | curated cyanobacterial metabolites |
Measured bioactivity and molecular targets come from a fifth and sixth source, both verified the same day: BindingDB's own-curated subset (CC BY 3.0, and separable from its ChEMBL-derived records by a provenance column) and PubChem BioAssay (public domain, recorded per depositor).
Excellent resources that cannot be seeded into a CC BY 4.0 corpus, and why: NPAtlas (CC BY-NC from release 2024_09), Norine (CC BY-NC-SA), NP-MRD (CC BY-NC), CMNPD (CC BY-NC-SA), NPBS Atlas (CC BY-NC), IMPPAT and DrugBank (non-commercial), KNApSAcK (redistribution prohibited), ChEMBL, DrugCentral and the Guide to PHARMACOLOGY (share-alike), ClassyFire/ChemOnt (bespoke terms), MetaCyc (subscription), KEGG (not a public database). NPASS, the Therapeutic Target Database and StreptomeDB state no licence at all, which is not the same as permission, and CO-ADD reserves all rights while calling itself open-access. COCONUT advertises CC0 over a collection that demonstrably contains rows from several of the restricted sources above.
The full reasoning, with licence text quoted from each primary page, is in the research report.
See the native merge queue guide for PR checks, queue validation, and recovery when a queued change fails.
Project-authored data, records, annotations, mappings, data exports and narrative documentation are licensed under CC BY 4.0. Project-authored code, scripts, tests, schemas and website templates are licensed under BSD-3-Clause. See LICENSE for scope and attribution.
Third-party material retains its own licenses and notices. Preserve upstream attribution and source-specific terms when redistributing a record or subset. Previously released material remains available under its original license.