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alterlab-reactome

Query Reactome pathways and analyses via ContentService and AnalysisService REST APIs.

58|9|Updated Mar 16, 2026
Search Tags:#python#bioinformatics#enrichment#rest-api#reactome#pathway-analysis
One-click install
npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-reactome
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alterlab-reactome
Source: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/databases/alterlab-reactome
Command: npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-reactome

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Query and analyze Reactome data programmatically by accessing the ContentService and AnalysisService REST APIs.

Core Features & Use Cases

  • Content & Entity Queries: Retrieve pathway information, participating entities, and pathway definitions using REST endpoints.
  • Pathway Analysis & Visualization: Perform overrepresentation and expression analyses, manage analysis tokens, and view results in the Pathway Browser.
  • CLI + Library Support: Use the Python CLI (scripts/reactome_query.py) to automate common tasks and integrate with pipelines.

Quick Start

Use the Reactome CLI (scripts/reactome_query.py) to query a pathway by ID or perform enrichment analysis on a gene list.

Frequently Asked Questions about alterlab-reactome

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

FAQPage Schema
How do I programmatically query Reactome pathway data in Python?▼

You can query Reactome pathway data programmatically using a Python CLI that accesses the ContentService REST API to retrieve pathway information and participating entities.

How do I perform overrepresentation and expression analysis on a gene list with Reactome?▼

Perform overrepresentation and expression analyses on a gene list by submitting data to the Reactome AnalysisService REST API, which generates tokens for viewing results in the Pathway Browser.

Can I automate Reactome enrichment analysis and integrate it into a bioinformatics pipeline?▼

Yes, you can automate Reactome enrichment analysis within bioinformatics pipelines by using the provided Python CLI and the requests library to execute REST API calls.

Do I need the requests library to run Reactome API queries in Python?▼

Yes, the requests library is required as the core dependency for executing REST API calls to the Reactome ContentService and AnalysisService endpoints.

What is the best way to visualize Reactome pathway analysis results from a script?▼

The best way to visualize Reactome pathway analysis results from a script is by using the generated analysis tokens to load and display results directly in the Reactome Pathway Browser.

Does this Reactome Python CLI support species mapping for pathway analysis?▼

Yes, the Reactome Python CLI supports species mapping alongside pathway information retrieval and enrichment workflows across typical bioinformatics analysis tasks.

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