skills.rest
Imad-Oute
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reactome-database

Query Reactome pathways and perform enrichment analysis via REST API.

Updated May 10, 2026
Search Tags:#bioinformatics#enrichment#reactome#pathway-analysis#gene#pathway#systems-biology
One-click install
npx skills add https://github.com/Imad-Oute/ResearchForge --skill reactome-database-imad-oute
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/Imad-Oute/ResearchForge/tree/main/OpenSource-Projects/claude-scientific-skills/scientific-skills/reactome-database
Command: npx skills add https://github.com/Imad-Oute/ResearchForge --skill reactome-database-imad-oute

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Researchers and bioinformaticians need to access detailed pathway information and conduct enrichment analyses for systems biology studies.

Core Features & Use Cases

  • Data Retrieval: Query and extract pathway details, molecular interactions, and participating entities from Reactome's curated database.
  • Pathway Analysis: Perform enrichment and overrepresentation analyses on gene or protein lists, or expression data.
  • Use Case: For example, analyze a list of differentially expressed genes to identify significantly involved biological pathways, or query specific pathways to understand their components and functions.

Quick Start

Use this Skill to perform pathway enrichment analysis on your gene list using Reactome's REST API.

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 list of differentially expressed genes?▼

Pathway enrichment analysis identifies significantly involved biological pathways from gene lists. This Skill queries the Reactome knowledgebase via REST API and Python client to perform overrepresentation analysis on your expression datasets.

What is Reactome pathway analysis and when do I need it for systems biology research?▼

Reactome pathway analysis retrieves curated biological pathway data and molecular interactions. You need it to interpret gene or protein lists in systems biology by identifying active pathways and participating entities.

Can I use Python to query the Reactome database for automated bioinformatics workflows?▼

Yes, you can query the Reactome database using Python. This Skill supports REST API calls and the reactome2py client library to automate data retrieval and extract pathway details programmatically.

Do I need requests and reactome2py to retrieve molecular interaction data from Reactome?▼

Yes, you need the requests and reactome2py libraries. These dependencies handle the REST API interactions required to retrieve pathway details, molecular interactions, and participating entities.

What's the best way to extract pathway details and participating entities from a curated biological database?▼

The best way to extract pathway details is using a programmatic REST API client. This Skill queries Reactome's curated database to retrieve specific pathways, components, and molecular functions efficiently.

What are the limitations of using REST API calls for pathway overrepresentation analysis?▼

REST API calls for pathway overrepresentation analysis require stable network connectivity and proper handling of response payloads. Automated workflows depend on external API rate limits and the accuracy of the curated Reactome knowledgebase.

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