tooluniverse-chemical-compound-retrieval - Claude MCP Skill

# 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

```python
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:

```python
# 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)

```python
# 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)

```python
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

```python
# 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.

```markdown
# 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]
```

---

## 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:
```markdown
**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 |