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tooluniverse-toxicology

Assess drug and chemical toxicity via adverse outcome pathways, FAERS signals, FDA labels, and toxicogenomics.

1.7k|254|Updated Mar 3, 2025
Search Tags:#signal detection#toxicology#drug safety#faers#adverse outcome pathway#toxicogenomics#fda labels
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-toxicology
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-toxicology
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-toxicology
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-toxicology

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Evaluating a drug or chemical's toxicity requires pulling evidence from many disconnected sources — mechanistic pathways, real-world adverse event reports, regulatory labels, and gene-disease databases — and synthesizing them into a defensible risk assessment. This Skill automates that multi-source toxicology workflow and produces a graded, integrated report.

Core Features & Use Cases

  • Adverse Outcome Pathway Mapping: Query AOPWiki to trace molecular initiating events through key events to apical outcomes with biological plausibility scores.
  • Real-World Signal Detection: Quantify FAERS adverse event signals with PRR/ROR disproportionality statistics and serious-event filtering.
  • Regulatory & Toxicogenomic Evidence: Extract FDA boxed warnings and contraindications from DailyMed, plus chemical-gene and chemical-disease associations from CTD.
  • Use Case: Ask for a hepatotoxicity assessment of a candidate compound and receive a structured report triangulating AOP mechanisms, FAERS signal strength, label warnings, and CTD gene targets with a final CRITICAL-to-LOW risk tier.

Quick Start

Generate a full toxicology report for acetaminophen covering AOP mechanisms, FAERS signals, FDA label warnings, and CTD toxicogenomic associations.

Frequently Asked Questions about tooluniverse-toxicology

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I assess drug toxicity using adverse outcome pathways?▼

Query AOPWiki_list_aops with an organ or mechanism keyword, then retrieve full pathway details with AOPWiki_get_aop. The workflow extracts the molecular initiating event, ordered key events, apical outcome, and biological plausibility score for each relevant AOP.

How to detect adverse event signals in FAERS data?▼

Use FAERS_count_reactions_by_drug_event to get top reactions, then FAERS_calculate_disproportionality to compute PRR and ROR with confidence intervals. Signals with PRR above 2 and at least 3 cases are considered meaningful; serious events can be filtered separately.

Can this workflow analyze environmental chemicals without FDA labels?▼

Yes, but DailyMed label mining applies only to FDA-approved drugs. For environmental chemicals, the workflow relies on AOPWiki pathway data and CTD chemical-gene-disease associations, and explicitly documents the missing regulatory label data.

What is the difference between AOP mechanisms and FAERS signals?▼

AOPWiki provides mechanistic hypotheses linking molecular events to adverse outcomes, while FAERS provides real-world statistical signals from reported adverse events. The skill treats them as distinct evidence types and grades each with a T1-T4 evidence tier.

What are the limitations of FAERS-based toxicity analysis?▼

FAERS data is observational and subject to confounding by indication and underreporting bias. Disproportionality signals indicate association, not causation, so the workflow cross-validates them against AOP mechanisms, FDA labels, and CTD evidence.

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