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skill CX Codex GP ChatGPT official · OpenAI

reactome-skill — Codex skill: what it does, how to install

Queries Reactome ContentService for biological pathways, reactions, and participants. Returns concise markdown summaries directly in Codex.

Install into Codex · Skills CLI (Vercel) All methods and platforms ↓ 
npx skills add openai/plugins --skill reactome-skill -a codex
Open on GitHub

What reactome-skill does

This skill queries the Reactome ContentService using an internal helper script scripts/rest_request.py. It passes a JSON payload via standard input to fetch pathway memberships, entity lookups, and diagram data. The agent outputs a short markdown summary instead of unparsed payloads.

Python must be installed locally to execute the script. The tool can limit list sizes with max_items=10 and save complete unformatted API outputs using the save_raw parameter. The raw payload path is reported back if exported.

Install this skill if your workflow involves querying biological databases during development. Skip it if you do not handle molecular pathway data.

What it helps with

  • fetch biological pathway summaries by event identifier
  • list molecular participants for a reaction
  • save complete Reactome endpoint responses directly to disk

Example prompts for the agent

  • Look up participants for event R-HSA-199420 in Reactome
  • Find low-level pathways for entity P38398 in Homo sapiens

How to install reactome-skill

1Skills CLI (Vercel)

npx skills add openai/plugins --skill reactome-skill -a codex

2Manually: put the files in place

.agents/skills/reactome-skill/SKILL.md

For all projects use ~/.agents/skills/

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Questions about reactome-skill

How to install reactome-skill in Codex?

Run npx skills add openai/plugins --skill reactome-skill in your terminal.

What does reactome-skill do?

It queries the Reactome ContentService to retrieve concise pathway and molecular participant summaries.

What are the runtime requirements?

It requires a working Python installation to execute scripts/rest_request.py.

See also

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