SkillsAdd

mims-harvard/tooluniverse

tooluniverse-chemical-compound-retrieval

Retrieve chemical compound data from PubChem and ChEMBL with disambiguation, cross-referencing, and stereochemistry handling.

First seen Feb 4, 2026

Installation

$ npx skills add mims-harvard/tooluniverse --skill tooluniverse-chemical-compound-retrieval
View on skills.sh ↗ GitHub repository ↗

Summary

  • 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).

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Also in this package

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npx skills add mims-harvard/tooluniverse
tooluniverse-sequence-retrieval 1.6K tooluniverse-literature-deep-research 643 tooluniverse-image-analysis 637 tooluniverse-clinical-guidelines 466 tooluniverse 458 tooluniverse-drug-research 452 tooluniverse-clinical-trial-design 440 tooluniverse-drug-drug-interaction 432 setup-tooluniverse 427 tooluniverse-disease-research 419

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More details

Agent compatibility

Declared targets from SKILL.md / docs. Unmarked agents are not listed — the skill may still install via the CLI.

Claude Code Not declared
Cursor Not declared
Codex Not declared
GitHub Copilot Not declared
Windsurf Not declared
Gemini CLI Not declared
Cline Not declared
OpenCode Not declared

Repository health

Stars 1.7K
License LICENSE
Default branch main
Open issues 9
Status Active

Package contents

Files included with this skill beyond the listing page.

  • skill md SKILL.md 4,613 B
  • docs SUMMARY.md 512 B

History

  1. First seen on skills.sh
  2. First recorded snapshot · 400 installs

SKILL.md

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: PubChemgetcompoundpropertiesbyCID, PubChemBioAssaygetassaysummary, PubChemToxgetacuteeffects, PubChemgetcompound2Dimageby_CID

ChEMBL: ChEMBLgetcompoundrecordactivities, ChEMBLgetmoleculetargets, ChEMBLgetassayactivities

Optional: PubChemgetassociatedpatentsbyCID, PubChemsearchcompoundsby_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) OPSINnametostructure → SMILES/InChIKey → PubChemgetCIDby_SMILES
PubChem name lookup ChEMBL search → SMILES → PubChemgetCIDbySMILES
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/smilesverifier.py --smiles "SMILESSTRING". Invalid SMILES produce wrong results or cryptic errors.

Tool Reference

PubChem: PubChemgetCIDbycompoundname, PubChemgetCIDbySMILES, PubChemgetcompoundpropertiesbyCID, PubChemgetcompound2DimagebyCID, PubChemBioAssaygetassaysummary, PubChemToxgetacuteeffects, PubChemgetassociatedpatentsbyCID, PubChemsearchcompoundsbysimilarity, PubChemsearchcompoundsby_substructure

ChEMBL: ChEMBLsearchdrugs, ChEMBLgetmolecule, ChEMBLgetactivity, ChEMBLgettarget, ChEMBLsearchtargets, ChEMBLsearchassays

Name parsing: OPSINnameto_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).