Tools

Eight tools — five for the ChEMBL compound/target/bioactivity surface, plus three for SQL analytics over the DuckDB-backed canvas that chembl_get_bioactivities spills to (the third is opt-in):

chembl_search_molecules

The discovery entry point for compounds.

• Default search_type=name matches drug names, synonyms, ChEMBL IDs, and InChIKeys in one query
• A query that is exactly a ChEMBL ID or an InChIKey is routed to ChEMBL's single-record lookup rather than the fuzzy text index, so it returns totalCount: 1 instead of a full-text relevance count. Adding max_phase_min returns the query to the text index, since that filter belongs to the search endpoint
• Structure search via search_type: exact (exact match), similarity (Tanimoto ≥ threshold), or substructure (contains the query structure) — supply structure as a SMILES
• similarity_threshold is an integer 40–100 (default 70; ChEMBL rejects values below 40)
• max_phase_min restricts name searches to compounds at or above a max clinical phase (e.g. 4 for marketed drugs only)
• Every row carries max_phase — the cheap druggability signal (4 = marketed, 0 = research) — plus MW, AlogP, Lipinski rule-of-five violations, and QED. Only search_type=similarity carries a Tanimoto similarity percent; exact and substructure results omit the field entirely, because ChEMBL supplies a score for similarity search alone
• Results past limit are reachable: when more remain, the response carries a nextCursor, and passing it back as cursor returns the following page. It is omitted — not null — on the last page. Redeem a cursor with the same filters that minted it
• Chain molecule_chembl_id into chembl_get_bioactivities or chembl_get_drug_info

chembl_get_bioactivities

The flagship tool and the reason the server exists — the curated compound↔target↔assay link.

• Supply at least one of molecule_chembl_id (target deconvolution / selectivity) or target_chembl_id (lead finding); supplying both narrows to that compound–target pair — "how potently does this compound hit this target, and in which assays?" — while neither is a missing_filter error
• Filter by standard_type (IC50 / Ki / EC50 / …), minimum potency pchembl_value_min, assay_type, and organism; rows are ranked on pchembl_value (−log10 molar potency)
• Ranking trap: pchembl_value is comparable only within one standard_type — set the filter, because mixing IC50 and Ki is a scientific error
• Coverage trap: many measurements have no derivable pchembl_value (non-standard types, censored relations) and are absent from the ranked view — aspirin CHEMBL25 has 4,087 measurements but only 158 with a pchembl_value. potency_view picks the side you get: potency_ranked (default) or null_potency for exactly the excluded rows. totalCount spans both either way. The two are separate calls, not one merged stream, because ChEMBL sorts null-potency rows first under a descending potency sort
• Numerics are coerced from upstream JSON strings to number | null at the service boundary — a missing potency reads as null, never 0
• A popular target carries tens of thousands of measurements: when the set exceeds the inline preview it spills to a DataCanvas table — call chembl_dataframe_describe for its columns, then chembl_dataframe_query for honest aggregates across the staged set — while the inline preview answers the immediate question. Each view stages its own table (bioactivities / bioactivities_null_potency), so running both against one canvas_id lets a UNION ALL rebuild the full set
• The staged table is capped at CHEMBL_MAX_SPILL_ROWS (default 50,000), which also bounds the upstream page walk behind it. When the cap is hit, truncated: true and staged_row_count say so on both response surfaces — the table is a bounded slice, not the complete view; narrow with standard_type / pchembl_value_min to fit
• The inline rows are always capped at limit (default 25) — spilled, fit inline, or canvas off — so compare that count against totalCount before treating them as the whole answer. Spilling the rest requires CANVAS_PROVIDER_TYPE=duckdb; without it the inline preview is all there is
• The optional canvas_id reuses an existing canvas, but a view's table is always re-registered — a second query of the same view replaces its prior rows rather than appending; omit canvas_id to mint a fresh one

chembl_search_targets

Resolve a protein into the ChEMBL target ID downstream tools need.

• Supply at least one of accession (UniProt, e.g. P00533), gene_symbol (e.g. EGFR), or query (free-text name); narrow further with organism and target_type
• A UniProt accession is the most precise input — chain it from a uniprot / protein server
• Each row carries the target type, organism, and component UniProt accessions + gene symbols (flattened from ChEMBL's nested component synonyms)
• Results past limit are reachable the same way chembl_search_molecules does it — a nextCursor when more remain, passed back as cursor, omitted on the last page
• Chain target_chembl_id into chembl_get_bioactivities

chembl_get_drug_info

Drug pharmacology for a molecule — distinct from the openfda server's label / adverse-event view.

• Supply molecule_chembl_id (from chembl_search_molecules)
• Returns mechanism(s) of action, the molecular target(s), action type (inhibitor / agonist / …), first-approval year, and clinical indications with the max phase reached for each
• Composed from molecule + mechanisms + indications with Promise.allSettled, so a rejected mechanism or indication list degrades to a disclosed partial result rather than failing the call
• Each list carries its own retrieval state — mechanisms_status / indications_status (complete / truncated / failed) next to mechanisms_total_count / indications_total_count, so an empty array is authoritative only when the status is complete
• A mechanism's target_chembl_id chains into chembl_get_bioactivities for compounds hitting the same target

chembl_get_assay