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reactome-database

Query Reactome REST APIs for pathway data and enrichment analyses.

21|1|Updated Mar 19, 2026
Search Tags:#bioinformatics#enrichment#rest-api#reactome#pathway-analysis#gene-list#pathway
One-click install
npx skills add https://github.com/OwnLabAI/ownlab --skill reactome-database-ownlabai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/reactome-database
Command: npx skills add https://github.com/OwnLabAI/ownlab --skill reactome-database-ownlabai

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Reactome-database enables researchers to programmatically access Reactome's pathway data and analytical services, turning manual queries into automated analyses.

Core Features & Use Cases

  • Content Service data retrieval and lookup for pathways, reactions, and entities.
  • Pathway enrichment and expression analysis via the Analysis Service for gene lists.
  • Python client and helper scripts to query pathways, fetch versions, and map genes to pathways.

Quick Start

Use the included Python scripts to query a pathway or run enrichment analysis on a gene list.

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 using Reactome?▼

Pathway enrichment analysis on a gene list is performed by submitting data to the Reactome Analysis Service. This Skill automates querying the REST API to retrieve overrepresentation results and map genes to human biological pathways.

Can I retrieve Reactome pathway data programmatically via a REST API?▼

Yes, Reactome pathway data can be retrieved programmatically using its REST API. This Skill queries the Content Service to fetch pathway details, reactions, and entities directly through reusable Python scripts.

What is pathway mapping and overrepresentation analysis in systems biology?▼

Pathway mapping and overrepresentation analysis identify statistically significant biological pathways within gene lists. This Skill uses the Reactome Analysis Service to automate expression data interpretation and systems biology research.

Does the Reactome REST API support token-based retrieval for enrichment results?▼

Yes, the Reactome REST API supports token-based result retrieval for enrichment analyses. This Skill manages token generation and data fetching automatically to retrieve expression analysis outcomes.

Do I need Python to automate Reactome pathway analysis queries?▼

Python is required to automate Reactome pathway analysis queries using this Skill. It provides reusable CLI scripts and helper functions that depend on the requests library to interact with the REST API.

What are the limitations of using the Reactome Analysis Service for expression data interpretation?▼

The Reactome Analysis Service is limited to human pathways for expression data interpretation. This Skill automates the REST API queries but does not modify the underlying database scope or analytical algorithms.

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