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Agent skill

Reactome Skill

by aipoch in aipoch/medical-research-skills

Query the Reactome REST API for pathway content and enrichment analyses; use when you need curated pathway data, reaction details, or overrepresentation results for a gene list.

MITAuto-check passedBackend & APIs

Install Reactome Skill

skills CLI
$ npx skills add aipoch/medical-research-skills --skill reactome-skill -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install aipoch/medical-research-skills reactome-skill --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/aipoch/medical-research-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/'scientific-skills/Evidence Insight/reactome-skill' .claude/skills/reactome-skill && rm -rf skills-src

Use ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.

Claude Code skills documentation · loads skills from .claude/skills/

Facts

Skill name
reactome-skill
GitHub stars
2k
Token cost
~681 tokens
SKILL.md length
256 words
Files
5 (incl. scripts, references)
Skills in repo
567
Repo updated
First seen
Licence
MIT

At a glance

Query the Reactome REST API for pathway content and enrichment analyses; use when you need curated pathway data, reaction details, or overrepresentation results for a gene list.

  • Works in 2 steps: Query pathway content by Reactome ID → Run overrepresentation analysis for a…
  • You need curated pathway data
  • SKILL.md covers When to Use, Key Features, Dependencies and Example Usage, plus 1 more section
  • Runs Python scripts from its folder; calls python and uv

What it does

Reactome Skill is an agent skill from aipoch/medical-research-skills. Query the Reactome REST API for pathway content and enrichment analyses; use when you need curated pathway data, reaction details, or overrepresentation results for a gene list.

Its SKILL.md is about 680 tokens, which your agent loads only when the skill is triggered. The skill folder holds 6 other files, including scripts and reference files (for example `reactome-skill_audit_result_v1.json`, `references/api_reference.md` and `scripts/reactome_tool.py`).

It sits in Backend & APIs, covering REST APIs. The repository describes itself as: Hundreds of agent skills for medical research, including protocol design, data analysis, evidence insights, and academic writing. The licence is MIT.

When your agent uses it

  • You need curated pathway data
  • Reaction details
  • Overrepresentation results for a gene list

Example prompts

  • “/reactome-skill”

Requirements

  • Python 3

Workflow steps

2 steps, taken from the step headings in SKILL.md.

  1. Query pathway content by Reactome ID
  2. Run overrepresentation analysis for a gene list

What it can do on your machine

Read from SKILL.md and the folder at commit 686e09d. It shows what the files ask for, not the result of running them.

  • Tool permissions

    Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.

    From allowed-tools in the SKILL.md frontmatter.

  • Runs code

    Ships 1 file in scripts/ (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python
    • uv

    From the folder's file list and the shell code blocks in SKILL.md.

  • Network

    Links to these hosts (documentation or services it may open):

    • reactome.org

    From URLs in SKILL.md, links to its own repository left out.

  • Credentials

    Names no API keys, tokens, secrets or passwords.

    From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.

Context cost

Reactome Skill loads about 681 tokens when it runs, and up to ~745 if it reads all its reference files. Until then it costs about 48 tokens; SKILL.md has 256 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~48
When it runs · the whole SKILL.md, loaded when a task matches
~681
With references · SKILL.md plus every file in references/, read only if the agent opens them
~745

Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.

Safety

Auto-check passed

The automated check found no risky patterns in SKILL.md.

Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); the scripts in this folder are not scanned.

SKILL.md

The full file from aipoch/medical-research-skills at commit 686e09d, republished under its MIT licence (© aipoch). 256 words, ~681 tokens.

Download SKILL.mdSave it as .claude/skills/reactome-skill/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.
name
reactome-skill
description
Query the Reactome REST API for pathway content and enrichment analyses; use when you need curated pathway data, reaction details, or overrepresentation results for a gene list.
license
MIT
author
AIPOCH

Source: https://github.com/aipoch/medical-research-skills

When to Use

  • You have a list of genes/proteins and want to run pathway overrepresentation (enrichment) analysis against Reactome.
  • You need to retrieve curated pathway content (hierarchy, reactions, participants) by Reactome stable IDs (e.g., R-HSA-69278).
  • You want to map expression values onto pathways to support pathway-level interpretation.
  • You need to project pathways across species/organisms using Reactome’s species projection capabilities.
  • You are building a systems biology workflow that requires programmatic access to Reactome via its REST API.

Key Features

  • Pathway enrichment (overrepresentation) for identifier lists.
  • Expression analysis by mapping expression data to Reactome pathways.
  • Content retrieval for pathways, reactions, and participating molecules.
  • Pathway hierarchy access to navigate curated pathway structures.
  • Species projection to map pathways across organisms.
  • API documentation reference: see references/api_reference.md.

Dependencies

  • python (3.x)
  • requests (latest compatible)
  • reactome2py (latest compatible)

Install:

bash
uv pip install reactome2py requests

Example Usage

The following commands are runnable examples using the provided CLI script.

1) Query pathway content by Reactome ID
bash
python scripts/reactome_tool.py query_content --id "R-HSA-69278"
2) Run overrepresentation analysis for a gene list
bash
python scripts/reactome_tool.py analyze_identifiers --identifiers "TP53,BRCA1"

Implementation Details

  • API access pattern: The skill uses the Reactome REST API (via reactome2py and/or direct HTTP calls with requests) to fetch pathway content and submit analyses.
  • Identifier input: Gene/protein identifiers are provided as a comma-separated string (e.g., TP53,BRCA1) and are submitted for overrepresentation analysis.
  • Stable IDs: Content retrieval expects Reactome stable identifiers (commonly formatted like R-HSA-xxxxx for human pathways).
  • Outputs: Results typically include pathway/reaction metadata and analysis outputs (e.g., enriched pathways with associated statistics), depending on the invoked action.
  • Reference: Reactome developer documentation is available at https://reactome.org/dev and the local API notes at references/api_reference.md.

© aipoch, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 4 other files (scripts, references) in scientific-skills/Evidence Insight/reactome-skill of aipoch/medical-research-skills.

  • SKILL.md
  • reactome-skill_audit_result_v1.json
  • references/api_reference.md
  • scripts/reactome_tool.py
  • skill_spec.yaml

Open the folder on GitHubat commit 686e09d

Compare with similar skills

Reactome Skill next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.

Reactome Skill compared with similar skills
SkillStarsUsed inTokensAuto-checkLicenceRepo updated
Reactome Skill this skillaipoch/medical-research-skills2k—~681Automated safety check: PassMIT
API DesignerJeffallan/claude-skills12k2 repos~2kAutomated safety check: PassMIT
Paperclippaperclipai/paperclip98k—~9.6kAutomated safety check: PassMIT
Nodejs Backend Patternsever-works/ever-works15817 repos~4kAutomated safety check: PassAGPL-3.0
OpenAPI to MCP Servermcp-use/mcp-use11k—~5.2kAutomated safety check: PassApache-2.0
Use Yaakmountain-loop/yaak19k—~1.9kAutomated safety check: PassMIT

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Categories

Questions about Reactome Skill

What does Reactome Skill do?

Query the Reactome REST API for pathway content and enrichment analyses; use when you need curated pathway data, reaction details, or overrepresentation results for a gene list. Reactome Skill is an agent skill from aipoch/medical-research-skills. Query the Reactome REST API for pathway content and enrichment analyses; use when you need curated pathway data, reaction details, or overrepresentation results for a gene list.

When should I use Reactome Skill?

Reactome Skill fits situations like: you need curated pathway data; reaction details; overrepresentation results for a gene list.

How do I install Reactome Skill in Claude Code?

Run `npx skills add aipoch/medical-research-skills --skill reactome-skill -a claude-code`. Or copy the skill folder (scientific-skills/Evidence Insight/reactome-skill in aipoch/medical-research-skills) into .claude/skills/reactome-skill in your project. Claude Code loads it when a task matches its description.

How do I install Reactome Skill in Codex?

Run `npx skills add aipoch/medical-research-skills --skill reactome-skill -a codex`. Or copy the skill folder (scientific-skills/Evidence Insight/reactome-skill in aipoch/medical-research-skills) into .agents/skills/reactome-skill in your project. Codex loads it when a task matches its description.

Can I use Reactome Skill in Cursor, Gemini CLI or GitHub Copilot?

Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add aipoch/medical-research-skills --skill reactome-skill -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/reactome-skill, .gemini/skills/reactome-skill, .github/skills/reactome-skill and .opencode/skills/reactome-skill in your project.

What does Reactome Skill need to run?

Going by SKILL.md and its folder, Reactome Skill needs Python for the scripts in its folder and the command-line tools its instructions call (python and uv). Our summary lists: Python 3.

Does Reactome Skill access the network?

SKILL.md names 1 domain. As links in the text: reactome.org. This is read from the text; nothing was executed.

Is Reactome Skill safe to install?

Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.

What licence does Reactome Skill use?

Reactome Skill is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Reactome Skill use?

About 681 tokens (SKILL.md is roughly 2.7k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 64 tokens, read only when the agent opens those files.

What are the alternatives to Reactome Skill?

Skills that share tags, products or a category with Reactome Skill: API Designer (Jeffallan/claude-skills, 12k stars), Paperclip (paperclipai/paperclip, 98k stars), Nodejs Backend Patterns (ever-works/ever-works, 158 stars) and OpenAPI to MCP Server (mcp-use/mcp-use, 11k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Reactome Skill?

aipoch (a GitHub organization) maintains it in aipoch/medical-research-skills, which has 1,973 GitHub stars. The repository holds 567 skills in this directory. The repository was last updated on September 17, 2026.

Source: aipoch/medical-research-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.