Chemical Compound Information Retrieval

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

IMPORTANT: Always use English compound names and search terms in tool calls, even if the user writes in another language (e.g., translate "阿司匹林" to "aspirin"). Only try original-language terms as a fallback if English returns no results. Respond in the user's language.

Workflow Overview

Phase 0: Clarify (if needed)
    ↓
Phase 1: Disambiguate Compound Identity
    ↓
Phase 2: Retrieve Data (Internal)
    ↓
Phase 3: Report Compound Profile

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Phase 0: Clarification (When Needed)

Ask the user ONLY if:

• Compound name is highly ambiguous (e.g., "vitamin E" → α, β, γ, δ-tocopherol?)
• Multiple distinct compounds share the name (e.g., "aspirin" is clear; "sterol" is not)

Skip clarification for:

• Unambiguous drug names (aspirin, ibuprofen, metformin)
• Specific identifiers provided (CID, ChEMBL ID, SMILES)
• Clear structural queries (SMILES, InChI)

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Phase 1: Compound Disambiguation

1.1 Resolve Primary Identifier

from tooluniverse import ToolUniverse
tu = ToolUniverse()
tu.load_tools()

# Strategy depends on input type
if user_provided_cid:
    cid = user_provided_cid
elif user_provided_smiles:
    result = tu.tools.PubChem_get_CID_by_SMILES(smiles=smiles)
    cid = result["data"]["cid"]
elif user_provided_name:
    result = tu.tools.PubChem_get_CID_by_compound_name(compound_name=name)
    cid = result["data"]["cid"]

1.2 Cross-Reference Identifiers

Always establish compound identity across both databases:

# PubChem → ChEMBL cross-reference
chembl_result = tu.tools.ChEMBL_search_compounds(query=compound_name, limit=5)
if chembl_result["data"]:
    chembl_id = chembl_result["data"][0]["molecule_chembl_id"]

1.3 Handle Naming Collisions