skills.rest
felixboehm
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reactome-database

Query the Reactome REST API for pathway enrichment and expression analysis.

Updated Mar 10, 2026
Search Tags:#bioinformatics#pathway analysis#systems biology#reactome#gene enrichment#molecular interactions
One-click install
npx skills add https://github.com/felixboehm/biochem-allergy --skill reactome-database-felixboehm
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/felixboehm/biochem-allergy/tree/main/.claude/skills/reactome-database
Command: npx skills add https://github.com/felixboehm/biochem-allergy --skill reactome-database-felixboehm

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides access to comprehensive biological pathway data and enables sophisticated pathway enrichment and expression analysis for systems biology research.

Core Features & Use Cases

  • Pathway Data Retrieval: Query Reactome's extensive database for pathway information, molecular interactions, and entity details.
  • Pathway Enrichment Analysis: Identify statistically significant biological pathways from gene or protein lists.
  • Expression Data Analysis: Analyze gene expression datasets to uncover relevant biological pathways.
  • Use Case: Given a list of differentially expressed genes from a transcriptomic study, use this Skill to identify the key biological pathways that are significantly altered in the condition being studied.

Quick Start

Use the reactome-database skill to perform pathway enrichment analysis on the gene list provided in 'my_genes.txt'.

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 altered biological pathways from gene lists. You provide a list of genes, and the Skill queries the Reactome REST API to map them to curated pathways and calculate statistical significance.

What is pathway enrichment and how does it work with the Reactome database?▼

Pathway enrichment uses the Reactome database to determine which biological pathways are over-represented in a given gene list. It works by querying curated molecular interactions and entity details via direct REST API calls to find statistically significant matches.

Can I query molecular interactions and entity details using Python?▼

Yes, you can query molecular interactions and entity details using Python. The Skill supports accessing Reactome's extensive database via direct REST API calls or a Python client to retrieve curated pathway information.

How do I analyze gene expression datasets to uncover relevant biological pathways?▼

To analyze gene expression datasets for relevant biological pathways, you use the Skill to perform expression analysis. It processes your dataset to map differentially expressed genes to curated pathways, revealing altered biological mechanisms.

Do I need the requests library to map genes to pathways?▼

Yes, you need the requests library. It is a required dependency for this Skill to execute direct API calls to the Reactome REST API, enabling the retrieval of pathway data and the mapping of genes to pathways.

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