Adverse Outcome Pathway (ToolUniverse Claude Skill)

A ToolUniverse agent skill that maps environmental and industrial chemicals to adverse outcome pathways — from molecular initiating event to organ-level toxicity — using AOPWiki, GHS classification, IARC carcinogen status, LD50 data, and toxicogenomics.


Type	Claude Skill (one of ToolUniverse’s pre-built agent skills)
Supplier	Zitnik Lab, Harvard Medical School
Availability	GA — part of the ToolUniverse skills collection (`skills/tooluniverse-adverse-outcome-pathway/`)
Pricing	Free / OSS (Apache-2.0); wraps public APIs (AOPWiki, PubChem, PubChemTox, CTD)
Capabilities	Read-only — drives ToolUniverse tool calls; no data writes
Verified	works · 2026-07-20
Security	cleared · 2026-07-20 — provenance matches Zitnik Lab, Apache-2.0, skill dir confirmed, no OSV advisories

How to install

This skill calls ToolUniverse tools, so the ToolUniverse MCP server must be installed first (see the ToolUniverse page). Simplest registration:

claude mcp add --transport stdio tooluniverse -- uvx tooluniverse

Then add the skills:

Claude Code — install the whole skill collection (the skill resolves as tooluniverse-adverse-outcome-pathway):
```
npx skills add mims-harvard/ToolUniverse
```
Manual / other agents — copy just this skill directory into your skills folder:
```
git clone https://github.com/mims-harvard/ToolUniverse
cp -r ToolUniverse/skills/tooluniverse-adverse-outcome-pathway ~/.claude/skills/
```
(replace ~/.claude/skills/ with your agent’s skills directory if you are not using Claude Code/Desktop.)

The skill sets disable-model-invocation: true upstream, so invoke it explicitly (e.g. ask Claude to “use the adverse-outcome-pathway skill”) rather than relying on automatic dispatch.

What it does

Runs a four-phase chemical hazard assessment:

Compound identity resolution — chemical names to PubChem CIDs (PubChem_get_CID_by_compound_name).
AOP discovery — search AOPWiki by organ, mechanism, or receptor; retrieve full pathway details including molecular initiating events, key events, and stressor lists (AOPWiki_list_aops, AOPWiki_get_aop).
Hazard quantification — parallel PubChemTox queries for GHS classification, IARC carcinogen status, and LD50/LC50 values (PubChemTox_get_ghs_classification, _get_carcinogen_classification, _get_toxicity_values).
Toxicogenomics integration — map chemicals to gene targets and disease associations via CTD, cross-referenced with AOP key-event genes (CTD_get_chemical_gene_interactions, CTD_get_chemical_diseases).

Primary use cases: mechanistic toxicity assessment, regulatory hazard screening, off-target/safety triage for candidate compounds.

Notes

It is a reasoning layer over ToolUniverse; without the MCP server registered, the tool calls fail. Aimed at environmental/industrial chemical toxicology, but the AOP + GHS/IARC + toxicogenomics surface is also useful for safety filtering in drug discovery. ToolUniverse ships ~150 such skills; other chemical-safety and drug-discovery workflows are catalogued separately.

Sources

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