mims-harvard/tooluniverse-chemical-compound-retrieval
plugin/skills/tooluniverse-chemical-compound-retrieval/SKILL.md
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 --global
skillsauthnpx skillsauth add mims-harvard/tooluniverse tooluniverse-chemical-compound-retrievalInstall this skill globally with one command. Works with Claude Code, Cursor, and Windsurf.
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SKILL.md
- name:
- tooluniverse-chemical-compound-retrieval
- description:
- 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).
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