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reactome-database

Query Reactome REST APIs to retrieve pathway data and perform enrichment analyses.

1|Updated Mar 11, 2026
Search Tags:#analysis#bioinformatics#pathways#enrichment#rest-api#reactome#gene
One-click install
npx skills add https://github.com/SciMate-AI/scicli --skill reactome-database-scimate-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/reactome-database
Command: npx skills add https://github.com/SciMate-AI/scicli --skill reactome-database-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) and references (resource) components.

What problem does it solve?

Researchers need programmatic access to Reactome's data and analysis services to retrieve pathways, map genes to pathways, and perform enrichment analyses without manual web interactions.

Core Features & Use Cases

  • REST API access to ContentService and AnalysisService for data retrieval and enrichment analyses
  • Query by pathway ID, search by name, and fetch participating entities
  • Run enrichment analyses with tokens and view results via the Pathway Browser
  • Lightweight CLI helper script for common Reactome operations

Quick Start

Run the reactome_query.py script with a pathway ID to fetch details and inspect results in the console.

Frequently Asked Questions about reactome-database

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

FAQPage Schema
How do I query Reactome pathways using a REST API?▼

To run Reactome gene enrichment analyses programmatically, this Skill submits gene lists to the AnalysisService and retrieves analysis tokens. These tokens allow you to access and view reproducible enrichment results across sessions via the Pathway Browser.

How do I map genes to pathways in Reactome?▼

To map genes to pathways in Reactome, this Skill submits your gene lists to the AnalysisService API. It processes the requests to map the genes and retrieves the corresponding pathway enrichment data directly in your console.

Can I use Python to access the Reactome ContentService and AnalysisService?▼

Yes, you can use Python to access the Reactome ContentService and AnalysisService. This Skill provides a bundled CLI script that utilizes the requests library to query pathway data, fetch entities, and run enrichment analyses.

Do I need internet access to perform Reactome pathway enrichment?▼

Yes, internet access is required to perform Reactome pathway enrichment because the Skill queries live Reactome REST APIs. You also need the Python requests library installed to execute the bundled CLI script successfully.

What is the best way to retrieve reproducible Reactome analysis results?▼

The best way to retrieve reproducible Reactome analysis results is by using analysis tokens. This Skill fetches these tokens from the AnalysisService API, ensuring your enrichment results can be consistently accessed and viewed in the Pathway Browser.

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