tooluniverse-chemical-compound-retrieval

researchmims-harvard

Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling. Use for resolving compound names to SMILES/InChI/CID/ChEMBL IDs (including OPSIN deterministic IUPAC-name-to-structure parsing), fetching molecular properties, distinguishing isomers/stereo forms, and cross-validating identity across databases. Always use English compound names; flags ambiguous queries (e.g., Vitamin D has multiple forms).

Install

npx skills add https://github.com/mims-harvard/tooluniverse --skill tooluniverse-chemical-compound-retrieval

SKILL.md

---name: tooluniverse-chemical-compound-retrievaldescription: Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling. Use for resolving compound names to SMILES/InChI/CID/ChEMBL IDs (including OPSIN deterministic IUPAC-name-to-structure parsing), fetching molecular properties, distinguishing isomers/stereo forms, and cross-validating identity across databases. Always use English compound names; flags ambiguous queries (e.g., Vitamin D has multiple forms).disable-model-invocation: true---

Chemical Compound Information Retrieval

Retrieve comprehensive chemical compound data with proper disambiguation and cross-database validation.

LOOK UP DON'T GUESS: Never assume a CID, ChEMBL ID, or molecular property value. Always retrieve from PubChem/ChEMBL.

English-first: Always use English compound names in tool calls. Respond in user's language.

Domain Reasoning: Disambiguation

"Aspirin" = one compound. "Vitamin D" = multiple forms (D2/D3/active metabolite). For generic class names (steroids, vitamins, acids), present candidates and confirm before proceeding.

Workflow

Phase 0: Clarify (only if highly ambiguous -- skip for unambiguous names or specific IDs)
Phase 1: Disambiguate → resolve PubChem CID + ChEMBL ID
Phase 2: Retrieve data (silent)
Phase 3: Report compound profile

Phase 1: Disambiguation

# By name
result = tu.tools.PubChem_get_CID_by_compound_name(compound_name=name)
# By SYSTEMATIC (IUPAC) name -> structure, deterministic parser (no DB lookup)
opsin = tu.tools.OPSIN_name_to_structure(name="2-acetoxybenzoic acid")
# Returns {parsed, smiles, inchi, inchikey}; use the SMILES/InChIKey to anchor a
# PubChem_get_CID_by_SMILES lookup. Trade/trivial names give parsed=false -> fall
# back to PubChem_get_CID_by_compound_name for those.
# By SMILES
result = tu.tools.PubChem_get_CID_by_SMILES(smiles=smiles)
# Cross-reference
chembl_result = tu.tools.ChEMBL_search_molecules(query=name, limit=5)

Verify: CID + ChEMBL ID + canonical SMILES + stereochemistry + salt forms.

Phase 2: Data Retrieval

PubChem: PubChem_get_compound_properties_by_CID, PubChemBioAssay_get_assay_summary, PubChemTox_get_acute_effects, PubChem_get_compound_2D_image_by_CID

ChEMBL: ChEMBL_get_compound_record_activities, ChEMBL_get_molecule_targets, ChEMBL_get_assay_activities

Optional: PubChem_get_associated_patents_by_CID, PubChem_search_compounds_by_similarity

Phase 3: Report

Compound Profile with: Identity (CID, ChEMBL ID, IUPAC, SMILES), Chemical Properties (MW, LogP, HBD, HBA, PSA, Lipinski), Bioactivity (targets, IC50/Ki), Drug Info (if approved), Data Sources.

Fallback Chains

Primary	Fallback
PubChem name lookup (systematic name)	`OPSIN_name_to_structure` → SMILES/InChIKey → PubChem_get_CID_by_SMILES
PubChem name lookup	ChEMBL search → SMILES → PubChem_get_CID_by_SMILES
ChEMBL bioactivity	PubChem bioassay summary
Drug label	Note "unavailable"

Evidence Grading

Grade	Criteria
Confirmed	CID + ChEMBL cross-match, InChI/SMILES agree
Probable	CID found, partial ChEMBL match
Uncertain	Single database only, or multiple CIDs
Unverified	No cross-reference, single-source

Bioactivity: ChEMBL > PubChem BioAssay for curated data. IC50/Ki < 100nM = potent, 100nM-1uM = moderate, >10uM = weak. Lipinski violations reduce oral bioavailability but don't disqualify.

SMILES Verification

Always verify novel SMILES: python3 src/tooluniverse/tools/smiles_verifier.py --smiles "SMILES_STRING". Invalid SMILES produce wrong results or cryptic errors.

Tool Reference

PubChem: PubChem_get_CID_by_compound_name, PubChem_get_CID_by_SMILES, PubChem_get_compound_properties_by_CID, PubChem_get_compound_2D_image_by_CID, PubChemBioAssay_get_assay_summary, PubChemTox_get_acute_effects, PubChem_get_associated_patents_by_CID, PubChem_search_compounds_by_similarity, PubChem_search_compounds_by_substructure

ChEMBL: ChEMBL_search_drugs, ChEMBL_get_molecule, ChEMBL_get_activity, ChEMBL_get_target, ChEMBL_search_targets, ChEMBL_search_assays

Name parsing: OPSIN_name_to_structure (param name) — deterministic IUPAC/systematic-name → SMILES/InChI/InChIKey parser; the go-to for resolving a systematic name to structure without a DB round-trip. Trade/trivial names return parsed=false (use PubChem name lookup for those).