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

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)

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

For generic names (e.g., "vitamin", "steroid", "acid"):

• Search returns multiple CIDs → present top matches with structures

• Verify SMILES/InChI matches user intent

• Note stereoisomers or salt forms if relevant

Identity Resolution Checklist:

• PubChem CID established

• ChEMBL ID cross-referenced (if exists)

• Canonical SMILES captured

• Stereochemistry noted (if relevant)

• Salt forms identified (if applicable)

Phase 2: Data Retrieval (Internal)

Retrieve all data silently. Do NOT narrate the search process.

2.1 Core Properties (PubChem)

Basic properties

props = tu.tools.PubChem_get_compound_properties_by_CID(cid=cid)

Bioactivity summary

bio = tu.tools.PubChem_get_bioactivity_summary_by_CID(cid=cid)

Drug label (if approved drug)

drug = tu.tools.PubChem_get_drug_label_info_by_CID(cid=cid)

Structure image

image = tu.tools.PubChem_get_compound_2D_image_by_CID(cid=cid)

2.2 Bioactivity Data (ChEMBL)

if chembl_id: # Detailed bioactivity activity = tu.tools.ChEMBL_get_bioactivity_by_chemblid(chembl_id=chembl_id)

# Protein targets
targets = tu.tools.ChEMBL_get_target_by_chemblid(chembl_id=chembl_id)

# Assay data
assays = tu.tools.ChEMBL_get_assays_by_chemblid(chembl_id=chembl_id)

2.3 Optional Extended Data

Patents (for drugs)

patents = tu.tools.PubChem_get_associated_patents_by_CID(cid=cid)

Similar compounds (for SAR)

similar = tu.tools.PubChem_search_compounds_by_similarity(cid=cid, threshold=85)

Fallback Chains

Primary Fallback Notes

PubChem_get_CID_by_compound_name ChEMBL_search_compounds → get SMILES → PubChem_get_CID_by_SMILES Name lookup failed

ChEMBL_get_bioactivity PubChem_get_bioactivity_summary ChEMBL ID unavailable

PubChem_get_drug_label_info Note "Drug label unavailable" Not an approved drug

Phase 3: Report Compound Profile

Output Structure

Present results as a Compound Profile Report. Hide all search process details.

Compound Profile: [Compound Name]

Identity

Chemical Properties

Molecular Descriptors

Structural Representation

• SMILES: CC(=O)Oc1ccccc1C(=O)O
• InChI: InChI=1S/C9H8O4/...

[2D structure image if available]

Bioactivity Profile

Summary

• Active in: [X] assays out of [Y] tested
• Primary Targets: [list top targets]
• Mechanism: [if known]

Key Target Interactions (from ChEMBL)

Drug Information (if applicable)

Clinical Status

Safety

• Black Box Warning: [Yes/No]
• Major Interactions: [if any]

Related Compounds (if retrieved)

Top 5 structurally similar compounds:

Data Sources

• PubChem: [CID link]
• ChEMBL: [ChEMBL ID link]
• Retrieved: [date]

Data Quality Tiers

Apply to data completeness assessment:

Tier Symbol Criteria

Complete ●●● All core properties + bioactivity + drug info

Substantial ●●○ Core properties + bioactivity OR drug info

Basic ●○○ Core properties only

Minimal ○○○ CID/name only, limited data

Include in report header:

Data Completeness: ●●● Complete (properties, bioactivity, drug data)

Completeness Checklist

Every compound profile MUST include these sections (even if "unavailable"):

Identity (Required)

• PubChem CID

• ChEMBL ID (or "N/A")

• IUPAC name

• Canonical SMILES

Properties (Required)

• Molecular formula

• Molecular weight

• LogP

• Lipinski rule assessment

Bioactivity (Required)

• Activity summary (or "No bioactivity data")

• Primary targets (or "Unknown")

Drug Info (If Approved Drug)

• Approval status

• Indication

• Drug class

Always Include

• Data sources with links

• Retrieval date

• Quality tier assessment

Common Use Cases

Drug Property Check

User: "Tell me about metformin" → Full compound profile with drug information emphasis

Structure Verification

User: "Verify this SMILES: CC(=O)Oc1ccccc1C(=O)O" → Disambiguation-focused profile, confirm identity

SAR Analysis

User: "Find compounds similar to ibuprofen" → Similarity search + comparative property table

Target Identification

User: "What proteins does gefitinib target?" → ChEMBL bioactivity emphasis with target list

Error Handling

Error Response

"Compound not found" Try synonyms, verify spelling, offer SMILES search

"No ChEMBL ID" Note in Identity section, continue with PubChem data

"No bioactivity data" Include section with "No bioactivity screening data available"

"API timeout" Retry once, note unavailable data with "(retrieval failed)"

Tool Reference

PubChem (Chemical Database)

Tool Purpose

PubChem_get_CID_by_compound_name

Name → CID

PubChem_get_CID_by_SMILES

Structure → CID

PubChem_get_compound_properties_by_CID

Molecular properties

PubChem_get_compound_2D_image_by_CID

Structure visualization

PubChem_get_bioactivity_summary_by_CID

Activity overview

PubChem_get_drug_label_info_by_CID

FDA drug labels

PubChem_get_associated_patents_by_CID

IP information

PubChem_search_compounds_by_similarity

Find analogs

PubChem_search_compounds_by_substructure

Substructure search

ChEMBL (Bioactivity Database)

Tool Purpose

ChEMBL_search_compounds

Name/structure search

ChEMBL_get_compound_by_chemblid

Compound details

ChEMBL_get_bioactivity_by_chemblid

Activity data

ChEMBL_get_target_by_chemblid

Protein targets

ChEMBL_search_targets

Target search

ChEMBL_get_assays_by_chemblid

Assay metadata