From mims-harvard-tooluniverse
Assesses chemical safety and toxicology integrating ADMET-AI predictions, CTD toxicogenomics, FDA labels, DrugBank profiles, and STITCH interactions. For toxicity profiling, ADMET properties, drug safety, and environmental risks.
npx claudepluginhub joshuarweaver/cascade-data-analytics --plugin mims-harvard-tooluniverseThis skill uses the workspace's default tool permissions.
**Toxicity assessment**: identify the chemical, check known hazards (GHS, IARC), then look for ADMET predictions. Dose makes the poison — always consider exposure level, as a compound that is toxic at high doses may be safe at relevant exposures. Distinguish between acute toxicity (LD50, GHS category) and chronic hazards (carcinogenicity, endocrine disruption) — they require different risk mana...
Conducts multi-round deep research on GitHub repos via API and web searches, generating markdown reports with executive summaries, timelines, metrics, and Mermaid diagrams.
Dynamically discovers and combines enabled skills into cohesive, unexpected delightful experiences like interactive HTML or themed artifacts. Activates on 'surprise me', inspiration, or boredom cues.
Generates images from structured JSON prompts via Python script execution. Supports reference images and aspect ratios for characters, scenes, products, visuals.
Toxicity assessment: identify the chemical, check known hazards (GHS, IARC), then look for ADMET predictions. Dose makes the poison — always consider exposure level, as a compound that is toxic at high doses may be safe at relevant exposures. Distinguish between acute toxicity (LD50, GHS category) and chronic hazards (carcinogenicity, endocrine disruption) — they require different risk management approaches. Computational predictions (ADMETAI) are T3 evidence and must be anchored by experimental data from PubChemTox or FDA labels wherever available. When evidence conflicts between prediction and experiment, always defer to the experimental finding.
LOOK UP DON'T GUESS: never assume GHS categories, IARC classification, or CTD disease links — always call PubChemTox and CTD tools to retrieve current classifications before reporting.
Comprehensive chemical safety analysis integrating predictive AI models, curated toxicogenomics databases, regulatory safety data, and chemical-biological interaction networks.
Triggers:
Use Cases:
When analysis requires computation (statistics, data processing, scoring, enrichment), write and run Python code via Bash. Don't describe what you would do — execute it and report actual results. Use ToolUniverse tools to retrieve data, then Python (pandas, scipy, statsmodels, matplotlib) to analyze it.
get_tool_info before calling unfamiliar tools| 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.
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.
PubChem_get_CID_by_compound_name (name: str)PubChem_get_compound_properties_by_CID (cid: int)ChEMBL_get_molecule (if ChEMBL ID available)Dependency: ADMET-AI tools require
pip install tooluniverse[ml]. If unavailable, skip to Phase 3 and use CTD + PubChemTox as alternatives.
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])ADMETAI_predict_BBB_penetrance / _bioavailability / _clearance_distribution / _CYP_interactions / _physicochemical_properties / _solubility_lipophilicity_hydration (all take smiles: list[str])CTD_get_chemical_gene_interactions (input_terms: str) — chemical name, returns gene interactions across speciesCTD_get_chemical_diseases (input_terms: str) — chemical-disease associations with evidence typePubChemTox_get_toxicity_values (cid: int) — LD50, LC50, NOAEL reference valuesPubChemTox_get_ghs_classification (cid: int) — GHS hazard classification and pictogramsPubChemTox_get_carcinogen_classification (cid: int) — NTP/IARC carcinogenicity assessmentsPubChemTox_get_acute_effects (cid: int) — acute toxicity by route/speciesPubChemTox_get_toxicity_summary (cid: int) — integrated toxicity overviewAOPWiki_list_aops (keyword: str) — search for relevant AOPs by chemical/mechanismAOPWiki_get_aop (aop_id: int) — full AOP detail: MIE, key events, adverse outcomeEnvironmental chemicals: Skip Phases 4-5 (no FDA labels/DrugBank). Use CTD + PubChemTox + AOPWiki instead.
FDA_get_boxed_warning_info_by_drug_name / _contraindications_ / _adverse_reactions_ / _warnings_ (all take drug_name: str)drugbank_get_safety_by_drug_name_or_drugbank_id (query, case_sensitive, exact_match, limit - all 4 required)STITCH_get_chemical_protein_interactions (identifiers: list[str], species: int)STRING_get_interaction_partners for key target genes (e.g., ESR1 for endocrine disruptors)DGIdb_get_drug_gene_interactions (genes: list[str]) — for target druggability contextChEMBL_search_compound_structural_alerts (molecule_chembl_id: str)| 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 |
# 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.
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