reactome-database

Identify enriched Reactome pathways from gene lists via REST APIs and reactome2py.

Updated Mar 30, 2026

Search Tags:#api #bioinformatics #enrichment #reactome #pathway-analysis #reactome2py #gene-list

Ready to run

npx skills add https://github.com/ya-way/cytoclaw-skills --skill reactome-database-ya-way

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/ya-way/cytoclaw-skills/tree/main/workspace/skills/labclaw-reactome-database
Command: npx skills add https://github.com/ya-way/cytoclaw-skills --skill reactome-database-ya-way

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, reactome2py, and includes scripts (resource) and references (resource) components.

What problem does it solve?

Reactome data enables researchers to perform pathway enrichment, gene-to-pathway mapping, and disease pathway exploration via REST APIs and a Python client, facilitating deeper interpretation of gene lists in systems biology studies.

Core Features & Use Cases

Enrichment analysis: identify overrepresented Reactome pathways for a given gene list.
Pathway mapping: translate gene or protein identifiers to Reactome pathways and interactions.
API integration: leverage Content Service, Analysis Service, and the reactome2py client for streamlined analyses.
Use Case: analyze RNA-seq derived gene lists to reveal biological processes driving observed phenotypes.

Quick Start

Provide a gene list file (one per line) and run the Reactome query script to obtain enriched pathways.

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 from RNA-seq data?▼

Pathway enrichment analysis identifies overrepresented Reactome pathways for a given gene list. You provide a gene list file and run the dedicated query script to obtain enriched pathways driving observed phenotypes.

How does gene-to-pathway mapping work in systems biology workflows?▼

Gene-to-pathway mapping translates gene or protein identifiers to Reactome pathways and interactions. It leverages REST API Content Service endpoints and the reactome2py Python client to retrieve biological pathway associations.

Can I use the reactome2py client to access Reactome Analysis Service endpoints?▼

Yes, the reactome2py client satisfies API access to both Content Service and Analysis Service endpoints. It enables streamlined Python workflows for querying disease pathways and performing cross-species comparisons.

What is the best way to explore disease pathways using Reactome APIs?▼

Exploring disease pathways via Reactome APIs involves using the Analysis Service to process gene lists and the Content Service to query pathway details. The reactome2py client streamlines these REST API calls for disease discovery.

Do I need a specific input format for gene list analysis with Reactome?▼

For gene list analysis, you provide a gene list file with one identifier per line. Running the Reactome query script with this file maps genes to pathways and returns the enrichment analysis results.

What are the limitations of using REST API calls for cross-species pathway comparisons?▼

REST API cross-species comparisons depend on Reactome's curated pathway coverage and identifier mappings within the Content Service. Limitations arise when species lack curated data or gene identifiers cannot be mapped.