Retrieves chemical compound information from PubChem and ChEMBL with disambiguation, cross-referencing, and quality assessment. Creates comprehensive compound profiles with identifiers, properties, bioactivity, and drug information. Use when users need chemical data, drug information, or mention PubChem CID, ChEMBL ID, SMILES, InChI, or compound names.
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.
Phase 0: Clarify (if needed)
↓
Phase 1: Disambiguate Compound Identity
↓
Phase 2: Retrieve Data (Internal)
↓
Phase 3: Report Compound Profile
Ask the user ONLY if:
Skip clarification for:
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"]
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"]
For generic names (e.g., "vitamin", "steroid", "acid"):
Identity Resolution Checklist:
Retrieve all data silently. Do NOT narrate the search process.
# 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)
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)
# 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)
| 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 |
Present results as a Compound Profile Report. Hide all search process details.
# Compound Profile: [Compound Name]
## Identity
| Property | Value |
|----------|-------|
| **PubChem CID** | [cid] |
| **ChEMBL ID** | [chembl_id or "N/A"] |
| **IUPAC Name** | [full name] |
| **Common Names** | [synonyms] |
## Chemical Properties
### Molecular Descriptors
| Property | Value | Drug-Likeness |
|----------|-------|---------------|
| **Formula** | C₉H₈O₄ | - |
| **Molecular Weight** | 180.16 g/mol | ✓ (<500) |
| **LogP** | 1.19 | ✓ (-2 to 5) |
| **H-Bond Donors** | 1 | ✓ (<5) |
| **H-Bond Acceptors** | 4 | ✓ (<10) |
| **Polar Surface Area** | 63.6 Ų | ✓ (<140) |
| **Rotatable Bonds** | 3 | ✓ (<10) |
### 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)
| Target | Activity Type | Value | Units |
|--------|--------------|-------|-------|
| [Target 1] | IC50 | [value] | nM |
| [Target 2] | Ki | [value] | nM |
## Drug Information (if applicable)
### Clinical Status
| Property | Value |
|----------|-------|
| **Approval Status** | [Approved/Investigational/N/A] |
| **Drug Class** | [therapeutic class] |
| **Indication** | [approved uses] |
| **Route** | [oral/IV/topical/etc.] |
### Safety
- **Black Box Warning**: [Yes/No]
- **Major Interactions**: [if any]
## Related Compounds (if retrieved)
Top 5 structurally similar compounds:
| CID | Name | Similarity | Key Difference |
|-----|------|------------|----------------|
| [cid] | [name] | 95% | [note] |
## Data Sources
- PubChem: [CID link]
- ChEMBL: [ChEMBL ID link]
- Retrieved: [date]
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)
Every compound profile MUST include these sections (even if "unavailable"):
User: "Tell me about metformin" → Full compound profile with drug information emphasis
User: "Verify this SMILES: CC(=O)Oc1ccccc1C(=O)O" → Disambiguation-focused profile, confirm identity
User: "Find compounds similar to ibuprofen" → Similarity search + comparative property table
User: "What proteins does gefitinib target?" → ChEMBL bioactivity emphasis with target list
| 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)" |
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 |