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tooluniverse-adverse-outcome-pathway

Maps environmental chemicals to adverse outcome pathways using AOPWiki, PubChemTox, and CTD data.

1.7k|254|Updated Mar 3, 2025
Search Tags:#toxicology#ghs classification#Risk Assessment#adverse outcome pathway#iarc carcinogen#aopwiki#toxicogenomics
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-adverse-outcome-pathway
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-adverse-outcome-pathway
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-adverse-outcome-pathway
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-adverse-outcome-pathway

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Regulatory risk assessment of environmental and industrial chemicals requires pulling together mechanistic pathway evidence, hazard classifications, and toxicogenomics data from multiple disconnected databases, which is slow and error-prone when done manually.

Core Features & Use Cases

  • AOP Discovery and Stressor Mapping: Search AOPWiki by organ, mechanism, or receptor keyword and retrieve full adverse outcome pathway details including molecular initiating events, key events, and chemical stressors.
  • Hazard Quantification: Retrieve GHS classification, IARC carcinogen status, LD50/LC50 values, and acute exposure effects from PubChemTox using a resolved PubChem CID.
  • Toxicogenomics Integration: Map chemicals to gene interactions and disease associations via CTD, then cross-reference gene targets with AOP key event genes for mechanistic confirmation.
  • Use Case: A researcher evaluating benzo[a]pyrene can confirm it as a stressor in AOP 58 (AhR activation to liver tumor), pull its IARC Group 1 carcinogen classification and LD50 values, and corroborate the mechanism through CTD gene-disease evidence.

Quick Start

Ask the agent to perform a regulatory risk assessment for an environmental chemical such as benzo[a]pyrene, including its adverse outcome pathways, GHS classification, and carcinogen status.

Frequently Asked Questions about tooluniverse-adverse-outcome-pathway

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

FAQPage Schema
How do I find adverse outcome pathways for a chemical?▼

Search AOPWiki with the AOPWiki_list_aops tool using an organ, mechanism, or receptor keyword, then retrieve full pathway details with AOPWiki_get_aop. Check whether your compound appears in the returned stressors list to confirm the association.

How do I get GHS classification and LD50 for a compound?▼

First resolve the compound name to a PubChem CID with PubChem_get_CID_by_compound_name, then call PubChemTox_get_ghs_classification and PubChemTox_get_toxicity_values with that CID. LD50 results are reported by route and species.

What is the difference between this skill and drug pharmacovigilance analysis?▼

This skill targets environmental and industrial chemicals using AOPWiki, GHS, IARC, and CTD data. FDA-approved drugs with FAERS adverse event signals and drug labels should be analyzed with the tooluniverse-pharmacovigilance or tooluniverse-toxicology skills instead.

How do I check if a chemical is an IARC carcinogen?▼

Call PubChemTox_get_carcinogen_classification with the compound's PubChem CID and filter the classifications for IARC sources. IARC Group 1 means confirmed carcinogen, 2A probable, 2B possible, and 3 not classifiable.

What should I do when AOPWiki returns no results for my keyword?▼

Broaden the search term from a specific mechanism to a general organ term, such as replacing a receptor name with liver or lung. If PubChemTox target organ data is empty, fall back to the narrative toxicity summary endpoint.

How is CTD evidence used alongside AOP data?▼

CTD chemical-gene interactions are cross-referenced with AOP key event genes to support the mechanistic link between a compound and an adverse outcome. Curated direct evidence entries carry more weight than inferred associations.

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