tooluniverse-chemical-compound-retrieval

```

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:

• 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)

---

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)

---

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 |

---

Output Structure

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

```markdown

# Compound Profile: [Compound Name]

| Property | Value |

|----------|-------|

| PubChem CID | [cid] |

| ChEMBL ID | [chembl_id or "N/A"] |

| IUPAC Name | [full name] |

| Common Names | [synonyms] |

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]

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 |

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]

Top 5 structurally similar compounds:

| CID | Name | Similarity | Key Difference |

|-----|------|------------|----------------|

| [cid] | [name] | 95% | [note] |

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

```

---

Apply to data completeness and reliability assessment:

Data Completeness

| 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 |

Data Reliability (Aligned with Research Skill Evidence Tiers)

| Tier | Symbol | Data Source | Reliability |

|------|--------|-------------|-------------|

| T1 | ★★★ | Experimental measurement (PubChem curated, ChEMBL assay) | High confidence |

| T2 | ★★☆ | Calculated/validated (computed but validated against experimental) | Good confidence |

| T3 | ★☆☆ | Predicted (ADMET-AI, computed without validation) | Use with caution |

| T4 | ☆☆☆ | Estimated/inferred (text-mined, database propagated) | Verify before use |

Include in report header:

```markdown

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

Data Reliability: Properties ★★★ (experimental), Bioactivity ★★★ (ChEMBL assays)

```

Apply Reliability Tiers to Properties

```markdown

Molecular Properties

| Property | Value | Reliability | Source |

|----------|-------|-------------|--------|

| Molecular Weight | 180.16 g/mol | ★★★ | PubChem (calculated) |

| LogP (experimental) | 1.19 | ★★★ | Measured |

| LogP (predicted) | 1.24 | ★★☆ | ADMET-AI |

| Solubility | 4.6 mg/mL | ★★★ | Experimental |

| Solubility (pred) | ~5 mg/mL | ★☆☆ | ADMET-AI prediction |

```

---

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

---

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 | 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 |