chemaudit-database-integrations

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.

# CAS number
curl -sS -X POST http://localhost:8000/api/v1/resolve \
  -H 'Content-Type: application/json' \
  -d '{"identifier": "50-78-2", "identifier_type": "auto"}'

# ChEMBL ID
curl -sS -X POST http://localhost:8000/api/v1/resolve \
  -H 'Content-Type: application/json' \
  -d '{"identifier": "CHEMBL25", "identifier_type": "auto"}'

# PubChem CID
curl -sS -X POST http://localhost:8000/api/v1/resolve \
  -H 'Content-Type: application/json' \
  -d '{"identifier": "2244"}'

# Compound name (OPSIN then PubChem)
curl -sS -X POST http://localhost:8000/api/v1/resolve \
  -H 'Content-Type: application/json' \
  -d '{"identifier": "acetylsalicylic acid"}'

# Explicit type hint
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"

1. Resolve the name first: POST /resolve {"identifier": "aspirin"} → get InChIKey.
2. POST /integrations/compare with the InChIKey → one consolidated response covering PubChem, ChEMBL, COCONUT.
3. 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"

1. Resolve to ChEMBL ID or InChIKey.
2. POST /integrations/chembl/bioactivity {"inchikey": "..."}.
3. 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.