tooluniverse-chemical-compound-retrieval

Install to Claude Code

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

Description

tooluniverse chemical compound retrieval

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

```python
# 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).