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Chemical Safety & Toxicology Assessment
Comprehensive chemical safety analysis integrating predictive AI models, curated toxicogenomics databases, regulatory safety data, and chemical-biological interaction networks.
When to Use This Skill
Triggers :
- "Is this chemical toxic?" / "Assess the safety profile of [drug/chemical]"
- "What are the ADMET properties of [SMILES]?"
- "What genes does [chemical] interact with?" / "What diseases are linked to [chemical] exposure?"
- "Drug safety assessment" / "Environmental health risk" / "Chemical hazard profiling"
Use Cases :
- Predictive Toxicology : AI-predicted endpoints (AMES, DILI, LD50, carcinogenicity, hERG) via SMILES
- ADMET Profiling : Absorption, distribution, metabolism, excretion, toxicity
- Toxicogenomics : Chemical-gene-disease mapping from CTD
- Regulatory Safety : FDA label warnings, contraindications, adverse reactions
- Drug Safety : DrugBank safety + FDA labels combined
- Chemical-Protein Interactions : STITCH-based interaction networks
- Environmental Toxicology : Chemical-disease associations for contaminants
KEY PRINCIPLES
- Report-first approach - Create report file FIRST, then populate progressively
- Tool parameter verification - Verify params via
get_tool_info before calling unfamiliar tools
- Evidence grading - Grade all safety claims by evidence strength (T1-T4)
- Citation requirements - Every toxicity finding must have inline source attribution
- Mandatory completeness - All sections must exist with data or explicit "No data" notes
- Disambiguation first - Resolve compound identity (name -> SMILES, CID, ChEMBL ID) before analysis
- Negative results documented - "No toxicity signals found" is data; empty sections are failures
- Conservative risk assessment - When evidence is ambiguous, flag as "requires further investigation"
- English-first queries - Always use English chemical/drug names in tool calls
Evidence Grading System (MANDATORY)
| Tier | Symbol | Criteria | Examples |
|---|
| T1 | [T1] | Direct human evidence, regulatory finding | FDA boxed warning, clinical trial toxicity |
| T2 | [T2] | Animal studies, validated in vitro | Nonclinical toxicology, AMES positive, animal LD50 |
| T3 | [T3] | Computational prediction, association data | ADMET-AI prediction, CTD association |
| T4 | [T4] | Database annotation, text-mined | Literature mention, unvalidated database entry |
Evidence grades MUST appear in: Executive Summary, Toxicity Predictions, Regulatory Safety, Chemical-Gene Interactions, Risk Assessment.
Core Strategy: 8 Research Phases
Chemical/Drug Query
|
+-- PHASE 0: Compound Disambiguation (ALWAYS FIRST)
| Resolve name -> SMILES, PubChem CID, ChEMBL ID, formula, weight
|
+-- PHASE 1: Predictive Toxicology (ADMET-AI)
| AMES, DILI, ClinTox, carcinogenicity, LD50, hERG, skin reaction
| Stress response pathways, nuclear receptor activity
|
+-- PHASE 2: ADMET Properties
| BBB penetrance, bioavailability, clearance, CYP interactions, physicochemical
|
+-- PHASE 3: Toxicogenomics (CTD)
| Chemical-gene interactions, chemical-disease associations
|
+-- PHASE 4: Regulatory Safety (FDA Labels)
| Boxed warnings, contraindications, adverse reactions, nonclinical tox
|
+-- PHASE 5: Drug Safety Profile (DrugBank)
| Toxicity data, contraindications, drug interactions
|
+-- PHASE 6: Chemical-Protein Interactions (STITCH)
| Direct binding, off-target effects, interaction confidence
|
+-- PHASE 7: Structural Alerts (ChEMBL)
| PAINS, Brenk, Glaxo structural alerts
|
+-- SYNTHESIS: Integrated Risk Assessment
Risk classification, evidence summary, data gaps, recommendations
See phase-procedures-detailed.md for complete tool parameters, decision logic, output templates, and fallback strategies for each phase.
Tool Summary by Phase
Phase 0: Compound Disambiguation
PubChem_get_CID_by_compound_name (name: str)PubChem_get_compound_properties_by_CID (cid: int)ChEMBL_get_molecule (if ChEMBL ID available)
Phase 1: Predictive Toxicology
ADMETAI_predict_toxicity (smiles: list[str]) - AMES, DILI, ClinTox, LD50, hERG, etc.ADMETAI_predict_stress_response (smiles: list[str])ADMETAI_predict_nuclear_receptor_activity (smiles: list[str])
Phase 2: ADMET Properties
ADMETAI_predict_BBB_penetrance / _bioavailability / _clearance_distribution / _CYP_interactions / _physicochemical_properties / _solubility_lipophilicity_hydration (all take smiles: list[str])
Phase 3: Toxicogenomics
CTD_get_chemical_gene_interactions (input_terms: str)CTD_get_chemical_diseases (input_terms: str)
Phase 4: Regulatory Safety
FDA_get_boxed_warning_info_by_drug_name / _contraindications_ / _adverse_reactions_ / _warnings_ / _nonclinical_toxicology_ / _carcinogenic_mutagenic_fertility_ (all take drug_name: str)
Phase 5: Drug Safety
drugbank_get_safety_by_drug_name_or_drugbank_id (query, case_sensitive, exact_match, limit - all 4 required)
Phase 6: Chemical-Protein Interactions
STITCH_resolve_identifier (identifier: str, species: 9606)STITCH_get_chemical_protein_interactions (identifiers: list[str], species: int, required_score: int)
Phase 7: Structural Alerts
ChEMBL_search_compound_structural_alerts (molecule_chembl_id: str)
Risk Classification Matrix
| Risk Level | Criteria |
|---|
| CRITICAL | FDA boxed warning OR multiple [T1] toxicity findings OR active DILI + active hERG |
| HIGH | FDA warnings OR [T2] animal toxicity OR multiple active ADMET endpoints |
| MEDIUM | Some [T3] predictions positive OR CTD disease associations OR structural alerts |
| LOW | All ADMET endpoints negative AND no FDA/DrugBank flags AND no CTD concerns |
| INSUFFICIENT DATA | Fewer than 3 phases returned data |
Report Structure
# Chemical Safety & Toxicology Report: [Compound Name]
**Generated**: YYYY-MM-DD | **SMILES**: [...] | **CID**: [...]
## Executive Summary (risk classification + key findings, all graded)
## 1. Compound Identity (disambiguation table)
## 2. Predictive Toxicology (ADMET-AI endpoints)
## 3. ADMET Profile (absorption, distribution, metabolism, excretion)
## 4. Toxicogenomics (CTD chemical-gene-disease)
## 5. Regulatory Safety (FDA label data)
## 6. Drug Safety Profile (DrugBank)
## 7. Chemical-Protein Interactions (STITCH network)
## 8. Structural Alerts (ChEMBL)
## 9. Integrated Risk Assessment (classification, evidence summary, gaps, recommendations)
## Appendix: Methods and Data Sources
See report-templates.md for full section templates with example tables.
Mandatory Completeness Checklist
- Phase 0: Compound disambiguated (SMILES + CID minimum)
- Phase 1: At least 5 toxicity endpoints or "prediction unavailable"
- Phase 2: ADMET A/D/M/E sections or "not available"
- Phase 3: CTD queried; results or "no data in CTD"
- Phase 4: FDA labels queried; results or "not FDA-approved"
- Phase 5: DrugBank queried; results or "not found"
- Phase 6: STITCH queried; results or "no data available"
- Phase 7: Structural alerts checked or "ChEMBL ID not available"
- Synthesis: Risk classification with evidence summary
- Evidence Grading: All findings have [T1]-[T4] annotations
- Data Gaps: Explicitly listed
Common Use Patterns
- Novel Compound : SMILES -> Phase 0 (resolve) -> Phase 1 (toxicity) -> Phase 2 (ADMET) -> Phase 7 (structural alerts) -> Synthesis
- Approved Drug Review : Drug name -> All phases (0-7) -> Complete safety dossier
- Environmental Chemical : Chemical name -> Phase 0 -> Phase 1-2 -> Phase 3 (CTD, key) -> Phase 6 (STITCH) -> Synthesis
- Batch Screening : Multiple SMILES -> Phase 0 -> Phase 1-2 (batch) -> Comparative table -> Synthesis
- Toxicogenomic Deep-Dive : Chemical + gene/disease interest -> Phase 0 -> Phase 3 (expanded CTD) -> Literature -> Synthesis
Limitations
- ADMET-AI : Computational [T3]; should not replace experimental testing
- CTD : May lag behind latest literature by 6-12 months
- FDA : Only covers FDA-approved drugs; not applicable to environmental chemicals
- DrugBank : Primarily drugs; limited industrial chemical coverage
- STITCH : Lower score thresholds increase false positives
- ChEMBL : Structural alerts require ChEMBL ID; not all compounds have one
- Novel compounds : May only have ADMET-AI predictions (no database evidence)
- SMILES validity : Invalid SMILES cause ADMET-AI failures
Reference Files
- phase-procedures-detailed.md - Complete tool parameters, decision logic, output templates, fallback strategies per phase
- evidence-grading.md - Evidence grading details and examples
- report-templates.md - Full report section templates with example tables
- phase-details.md - Additional phase context
- test_skill.py - Test suite
Summary
Total tools integrated : 25+ tools across 6 databases (ADMET-AI, CTD, FDA, DrugBank, STITCH, ChEMBL)
Best for : Drug safety assessment, chemical hazard profiling, environmental toxicology, ADMET characterization, toxicogenomic analysis
Outputs : Structured markdown report with risk classification (Critical/High/Medium/Low), evidence grading [T1-T4], and actionable recommendations
Weekly Installs
134
Repository
mims-harvard/to…universe
GitHub Stars
1.2K
First Seen
Feb 16, 2026
Security Audits
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Installed on
gemini-cli128
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