kohulan/chemaudit/chemaudit-database-integrations

Name: chemaudit-database-integrations
Author: kohulan

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kohulan/chemaudit
skills/chemaudit-database-integrations/SKILL.md
Updated 23 Sep 2026
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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).

Install

npx vskill@latest install kohulan/chemaudit/chemaudit-database-integrations

SKILL.md

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

bash

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:

json

{
  "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

bash

curl -sS -X POST http://localhost:8000/api/v1/integrations/chembl/bioactivity \
  -H 'Content-Type: application/json' \
  -d '{"inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"}'

Response:

json

{
  "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

bash

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:

json

{
  "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

bash

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

bash

curl -sS -X POST http://localhost:8000/api/v1/integrations/surechembl/lookup \
  -H 'Content-Type: application/json' \
  -d '{"inchikey": "BSYNRYMUTXBXSQ-UHFFFAOYSA-N"}'

Response:

json

{
  "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

bash

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:

json

{
  "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.

bash

# 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:

json

{
  "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.

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Source

SKILL.md in the repositoryCheckingskills/chemaudit-database-integrations/SKILL.md

Popularity

Repository stars: 63
Repository forks: 7
7-day trend score: 21

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Install

SKILL.md

ChemAudit Database Integrations

Overview

Workflow

1. PubChem

2. ChEMBL bioactivity

3. COCONUT natural products

4. Wikidata

5. SureChEMBL patent lookup

6. Cross-database comparison

7. Universal identifier resolver

Examples

Example 1 — "Look up aspirin in all databases"

Example 2 — "Convert this CAS number to SMILES"

Example 3 — "Has anyone filed a patent on this compound?"

Example 4 — "Get all ChEMBL bioactivity records for aspirin and filter to IC50 values in nM"

Example 5 — "Are the PubChem and ChEMBL SMILES consistent for this compound?"

Rate limits

Troubleshooting

found: false but the compound definitely exists in PubChem

/resolve: resolved: false, confidence: "none"

Slow Wikidata responses

/integrations/compare: verdict: "inconsistent"

ChEMBL returns 0 bioactivities for a known drug

SureChEMBL found: false but you know the compound is patented

Further reading

Security

Quality evaluation

Source

Popularity

Works with

`found: false` but the compound definitely exists in PubChem

`/resolve`: `resolved: false`, `confidence: "none"`

`/integrations/compare`: `verdict: "inconsistent"`

SureChEMBL `found: false` but you know the compound is patented