reactome-database

Query Reactome REST API for pathway enrichment and gene-pathway mapping.

Updated Mar 10, 2026

Search Tags:#bioinformatics #pathway analysis #systems biology #reactome #enrichment analysis #gene ontology

Ready to run

npx skills add https://github.com/Yezez9/Research-Agent --skill reactome-database-yezez9

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/Yezez9/Research-Agent/tree/main/scientific-skills/reactome-database
Command: npx skills add https://github.com/Yezez9/Research-Agent --skill reactome-database-yezez9

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill helps researchers and bioinformaticians understand complex biological processes by querying and analyzing data from the Reactome pathway database, making it easier to interpret experimental results and discover new biological insights.

Core Features & Use Cases

Pathway Enrichment Analysis: Identify significant biological pathways from gene or protein lists.
Gene-Pathway Mapping: Find which pathways a specific gene or protein is involved in.
Data Retrieval: Access detailed information about pathways, reactions, and molecular interactions.
Use Case: Given a list of differentially expressed genes from a RNA-seq experiment, use this Skill to find out which biological pathways are most affected, providing a high-level understanding of the cellular response.

Quick Start

Use the reactome-database skill to perform pathway enrichment analysis on the genes listed 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 differentially expressed genes?▼

You can perform pathway enrichment analysis by submitting a list of differentially expressed genes to the Reactome database via its REST API and Python client to identify significant biological pathways.

What is gene-pathway mapping in systems biology?▼

Gene-pathway mapping in systems biology finds which biological pathways a specific gene or protein is involved in by querying the Reactome database for molecular interaction data.

Can I use reactome2py to retrieve molecular interaction data for RNA-seq interpretation?▼

Yes, reactome2py and the Reactome REST API retrieve detailed molecular interaction data and reactions, providing a high-level understanding of cellular responses from RNA-seq experiments.

Does the Reactome database REST API support various identifier types for gene lists?▼

Yes, the Reactome REST API supports various identifier types and analysis methods to process gene lists and expression data for biological interpretation and pathway enrichment.

What is the best way to access biological pathway data for systems biology research?▼

Querying the Reactome database with a Python client like reactome2py is the best way to retrieve detailed biological pathway and molecular interaction data for systems biology research.

Why do I need both requests and reactome2py dependencies for pathway analysis?▼

You need requests and reactome2py to handle HTTP communication with the Reactome REST API and provide the Python client wrapper required to execute pathway enrichment analysis.