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reactome-database

Query Reactome REST APIs for pathway and enrichment data with Python.

4|1|Updated Jun 18, 2025
Search Tags:#python#analysis#enrichment#biomedical#reactome#gene-list#pathway
One-click install
npx skills add https://github.com/HolobiomicsLab/Toolomics --skill reactome-database-holobiomicslab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/HolobiomicsLab/Toolomics/tree/main/mcp_host/skills/scientific-skills/scientific-skills/reactome-database
Command: npx skills add https://github.com/HolobiomicsLab/Toolomics --skill reactome-database-holobiomicslab

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This skill provides programmatic access to Reactome REST APIs to retrieve pathway data, perform enrichment analyses, and map genes to pathways for systems biology studies.

Core Features & Use Cases

  • Query specific pathways and entities by ID using the Content Service.
  • Perform enrichment analyses and token-based retrieval via the Analysis Service.
  • Map gene lists to pathways and explore results for research workflows.
  • Use the included Python helper to automate common tasks.

Quick Start

Install dependencies and run the helper script to query Reactome data and perform analyses.

Frequently Asked Questions about reactome-database

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

FAQPage Schema
How do I perform pathway enrichment analysis on a gene list in Python?▼

Pathway enrichment analysis on a gene list in Python is performed by submitting data to the Reactome Analysis Service. The skill queries REST APIs to execute enrichment analyses and retrieve token-based results for systems biology research.

Can I map a list of genes to Reactome pathways programmatically?▼

Yes, you can map a list of genes to Reactome pathways programmatically using the included Python client and helper script. The skill retrieves gene-to-pathway mappings through the Reactome ContentService to explore entity participation.

How do I query Reactome for specific pathways and entities by ID?▼

Querying Reactome for specific pathways and entities by ID is done via the Content Service endpoints. The skill provides a Python helper to automate pathway lookup and entity retrieval for biomedical research workflows.

What dependencies do I need to access Reactome REST APIs with this tool?▼

You need the requests library installed to access Reactome REST APIs with this tool. The skill relies on this single Python dependency to handle HTTP requests for pathway information and enrichment results.

What is the best way to search Reactome pathways for biomedical research?▼

The best way to search Reactome pathways for biomedical research is using the skill's Python client to query the REST APIs. It supports pathway search, entity participation retrieval, and enrichment analyses across gene lists.

Does this skill support token-based retrieval for enrichment results?▼

Yes, this skill supports token-based retrieval for enrichment results via the Reactome AnalysisService. It leverages REST API endpoints to perform enrichment analyses and fetch results for gene lists.

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