| name | chemaudit-database-integrations |
| description | Look up molecules across PubChem, ChEMBL, COCONUT, Wikidata, and SureChEMBL patent databases, resolve chemical identifiers (CAS, ChEMBL ID, PubChem CID, ChEBI, UNII, DrugBank, names), and run cross-database consistency checks. Use when user says "look up in PubChem", "ChEMBL bioactivity", "natural product search", "COCONUT lookup", "Wikidata lookup", "resolve CAS number", "resolve ChEMBL ID", "cross-database check", "find this compound", "patent search", "SureChEMBL", or "identifier resolution". Supports SMILES, InChI, InChIKey, CAS, ChEMBL ID, PubChem CID, ChEBI, UNII, DrugBank ID, Wikipedia URL, and compound names (OPSIN + PubChem fallback).
|
| license | MIT |
| allowed-tools | Bash(curl:*) Bash(python:*) |
| compatibility | Requires a running ChemAudit instance with outbound network access to PubChem, ChEMBL, COCONUT, Wikidata, and SureChEMBL APIs.
|
| metadata | {"author":"Kohulan Rajan","version":"1.0.0","mcp-server":"chemaudit","category":"cheminformatics","tags":["PubChem","ChEMBL","COCONUT","Wikidata","identifier-resolution","databases","SureChEMBL"]} |
ChemAudit Database Integrations
Overview
Five external-database lookups plus two cross-database tools:
| Endpoint | Purpose |
|---|
POST /api/v1/integrations/pubchem/lookup | PubChem compound info (CID, IUPAC, synonyms, formula, MW) |
POST /api/v1/integrations/chembl/bioactivity | ChEMBL molecule + bioactivity records |
POST /api/v1/integrations/coconut/lookup | COCONUT natural-product database (>400K entries, organism, NP-likeness) |
POST /api/v1/integrations/wikidata/lookup | Wikidata via SPARQL (label, CAS, Wikipedia link) |
POST /api/v1/integrations/surechembl/lookup | SureChEMBL patent presence |
POST /api/v1/integrations/compare | Consistency check across PubChem + ChEMBL + COCONUT |
POST /api/v1/resolve | Universal identifier resolver for 11 identifier types |
All lookup endpoints accept {smiles: "...", inchikey: "..."} — provide at least one. Identifier resolution accepts anything.
Workflow
1. PubChem
curl -sS -X POST http://localhost:8000/api/v1/integrations/pubchem/lookup \
-H 'Content-Type: application/json' \
-d '{"smiles": "CC(=O)Oc1ccccc1C(=O)O"}'
Response:
{
"found": true,
"cid": 2244,
"iupac_name": "2-acetyloxybenzoic acid",
"molecular_formula": "C9H8O4",
"molecular_weight": 180.16,
"canonical_smiles": "CC(=O)OC1=CC=CC=C1C(=O)O",
"inchi": "InChI=1S/C9H8O4/c1-6(10)13-8-5-3-2-4-7(8)9(11)12/h2-5H,1H3,(H,11,12)",
"inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
"synonyms": ["aspirin", "acetylsalicylic acid", "2-acetoxybenzoic acid", ...],
"url": "https://pubchem.ncbi.nlm.nih.gov/compound/2244"
}
2. ChEMBL bioactivity
curl -sS -X POST http://localhost:8000/api/v1/integrations/chembl/bioactivity \
-H 'Content-Type: application/json' \
-d '{"inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"}'
Response:
{
"found": true,
"chembl_id": "CHEMBL25",
"pref_name": "ASPIRIN",
"molecule_type": "Small molecule",
"max_phase": 4,
"molecular_formula": "C9H8O4",
"molecular_weight": 180.16,
"canonical_smiles": "...",
"inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
"bioactivities": [
{
"target_chembl_id": "CHEMBL240",
"target_name": "Cyclooxygenase-1",
"target_type": "SINGLE PROTEIN",
"activity_type": "IC50",
"activity_value": 100.0,
"activity_unit": "nM",
"assay_chembl_id": "CHEMBL615139",
"document_chembl_id": "CHEMBL1127040"
}
],
"bioactivity_count": 1234,
"url": "https://www.ebi.ac.uk/chembl/compound_report_card/CHEMBL25"
}
max_phase: 0 (preclinical), 1-3 (clinical trials), 4 (approved).
3. COCONUT natural products
curl -sS -X POST http://localhost:8000/api/v1/integrations/coconut/lookup \
-H 'Content-Type: application/json' \
-d '{"smiles": "CN1C=NC2=C1C(=O)N(C(=O)N2C)C"}'
Response:
{
"found": true,
"coconut_id": "CNP0123456",
"name": "Caffeine",
"smiles": "CN1C=NC2=C1C(=O)N(C(=O)N2C)C",
"inchi": "...",
"inchikey": "RYYVLZVUVIJVGH-UHFFFAOYSA-N",
"molecular_formula": "C8H10N4O2",
"molecular_weight": 194.19,
"organism": "Coffea arabica",
"organism_type": "Plantae",
"nplikeness": 2.4,
"url": "https://coconut.naturalproducts.net/compounds/CNP0123456"
}
4. Wikidata
curl -sS -X POST http://localhost:8000/api/v1/integrations/wikidata/lookup \
-H 'Content-Type: application/json' \
-d '{"inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"}'
Returns label, canonical SMILES, InChIKey, CAS, formula, MW, and a Wikidata entity URL. SPARQL-based — typically slower than the other integrations. For a Wikipedia URL, use /resolve and read cross_references.wikipedia_url.
5. SureChEMBL patent lookup
curl -sS -X POST http://localhost:8000/api/v1/integrations/surechembl/lookup \
-H 'Content-Type: application/json' \
-d '{"inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"}'
Response:
{
"found": true,
"schembl_id": "SCHEMBL25",
"url": "https://www.surechembl.org/chemical/SCHEMBL25",
"patent_count": 8432,
"source": "unichem+surechembl",
"smiles": "...",
"inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
"molecular_weight": 180.16
}
Binary present/absent with direct link; patent count populated when SureChEMBL's enrichment API is reachable.
6. Cross-database comparison
curl -sS -X POST http://localhost:8000/api/v1/integrations/compare \
-H 'Content-Type: application/json' \
-d '{"inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"}'
At least one of smiles or inchikey required. Runs PubChem, ChEMBL, COCONUT in parallel and aligns outputs.
Response:
{
"entries": [
{"database": "PubChem", "found": true, "canonical_smiles": "...", "inchikey": "...", "molecular_formula": "C9H8O4", "molecular_weight": 180.16, "name": "...", "url": "..."},
{"database": "ChEMBL", "found": true, ...},
{"database": "COCONUT", "found": false, ...}
],
"comparisons": [
{"property_name": "canonical_smiles", "values": {"PubChem": "...", "ChEMBL": "..."}, "status": "agree", "detail": null},
{"property_name": "molecular_formula", "values": {"PubChem": "C9H8O4", "ChEMBL": "C9H8O4"}, "status": "agree", "detail": null},
{"property_name": "molecular_weight", "values": {"PubChem": "180.16", "ChEMBL": "180.159"}, "status": "minor_mismatch", "detail": "Difference within rounding tolerance"}
],
"overall_verdict": "consistent_minor",
"summary": "All databases agree on structural identity; minor numeric differences within tolerance."
}
Verdicts: consistent, consistent_minor (minor numeric differences), inconsistent (structural disagreement), no_data (no database found the compound).
7. Universal identifier resolver
Accepts 11 identifier types and resolves to canonical SMILES with cross-references. Use this before any other lookup when you don't know the structural representation.
curl -sS -X POST http://localhost:8000/api/v1/resolve \
-H 'Content-Type: application/json' \
-d '{"identifier": "50-78-2", "identifier_type": "auto"}'
curl -sS -X POST http://localhost:8000/api/v1/resolve \
-H 'Content-Type: application/json' \
-d '{"identifier": "CHEMBL25", "identifier_type": "auto"}'
curl -sS -X POST http://localhost:8000/api/v1/resolve \
-H 'Content-Type: application/json' \
-d '{"identifier": "2244"}'
curl -sS -X POST http://localhost:8000/api/v1/resolve \
-H 'Content-Type: application/json' \
-d '{"identifier": "acetylsalicylic acid"}'
curl -sS -X POST http://localhost:8000/api/v1/resolve \
-H 'Content-Type: application/json' \
-d '{"identifier": "DB00945", "identifier_type": "drugbank_id"}'
Supported types: auto, smiles, inchi, inchikey, pubchem_cid, chembl_id, cas, drugbank_id, chebi_id, unii, wikipedia, name.
Response:
{
"resolved": true,
"identifier_type_detected": "cas",
"canonical_smiles": "CC(=O)OC1=CC=CC=C1C(=O)O",
"inchi": "...",
"inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N",
"molecular_formula": "C9H8O4",
"molecular_weight": 180.16,
"iupac_name": "2-acetyloxybenzoic acid",
"resolution_source": "pubchem",
"resolution_chain": ["cas", "pubchem_cid", "smiles"],
"cross_references": {
"pubchem_cid": 2244,
"chembl_id": "CHEMBL25",
"coconut_id": null,
"drugbank_id": "DB00945",
"chebi_id": "CHEBI:15365",
"unii": "R16CO5Y76E",
"cas": "50-78-2",
"wikipedia_url": "https://en.wikipedia.org/wiki/Aspirin",
"kegg_id": "C01405"
},
"confidence": "high"
}
resolution_chain shows the UniChem/PubChem hops taken. confidence values: high, medium, low, none.
Examples
Example 1 — "Look up aspirin in all databases"
- Resolve the name first:
POST /resolve {"identifier": "aspirin"} → get InChIKey.
POST /integrations/compare with the InChIKey → one consolidated response covering PubChem, ChEMBL, COCONUT.- For patent info:
POST /integrations/surechembl/lookup separately.
Example 2 — "Convert this CAS number to SMILES"
Just one call: POST /resolve {"identifier": "50-78-2"} → returns canonical SMILES plus UniChem cross-references to all other databases.
Example 3 — "Has anyone filed a patent on this compound?"
POST /integrations/surechembl/lookup {"inchikey": "..."} → found tells you yes/no, patent_count tells you how many when enrichment API is available.
Example 4 — "Get all ChEMBL bioactivity records for aspirin and filter to IC50 values in nM"
- Resolve to ChEMBL ID or InChIKey.
POST /integrations/chembl/bioactivity {"inchikey": "..."}.bioactivities[] has per-record activity_type, activity_value, activity_unit. Filter client-side to activity_type=="IC50" and activity_unit=="nM".
Example 5 — "Are the PubChem and ChEMBL SMILES consistent for this compound?"
POST /integrations/compare with the InChIKey → comparisons[] has per-property agreement status. overall_verdict = "inconsistent" means structures disagree — worth investigating.
Rate limits
/integrations/pubchem/lookup, /chembl/bioactivity, /coconut/lookup, /wikidata/lookup, /surechembl/lookup: 30/min./integrations/compare: 10/min./resolve: 30/min.
Upstream APIs (PubChem, ChEMBL, etc.) have their own rate limits. Excessive queries may trigger temporary blocks from the upstream source — the ChemAudit service respects Retry-After headers where provided.
Troubleshooting
found: false but the compound definitely exists in PubChem
Try the other identifier. Some compounds are indexed by InChIKey but not easily queried by SMILES (and vice-versa) due to tautomer/isomer normalization on the upstream side. If /resolve finds it via name, use the returned InChIKey.
/resolve: resolved: false, confidence: "none"
None of the 11 resolvers matched. Common causes:
- Typo in the identifier.
- Non-standard format (e.g. CAS with no dashes).
- Compound is too new and hasn't been indexed in UniChem yet.
Slow Wikidata responses
SPARQL endpoint latency is highly variable. Wikidata is typically the slowest integration; consider skipping it for bulk workflows.
/integrations/compare: verdict: "inconsistent"
Structural disagreement across databases — usually a charge state, tautomer, or salt-form difference. Read comparisons[] to isolate which property differs. Often resolved by standardizing first (chemaudit-standardization) and re-querying.
ChEMBL returns 0 bioactivities for a known drug
Rare but possible when the compound is registered under a different ChEMBL ID (e.g. a salt form vs parent). /resolve the name, get the chembl_id from cross_references, then query directly.
SureChEMBL found: false but you know the compound is patented
UniChem's SureChEMBL cross-reference isn't comprehensive. When found-by-UniChem misses, the SureChEMBL direct API may still succeed — the service attempts both in sequence.
Further reading
chemaudit-molecule-validation — validate the structure once resolved.chemaudit-standardization — before cross-database comparison, standardize to reduce salt-form mismatches.chemaudit-dataset-intelligence — for dataset-level cross-database consistency checks.
