reactome-database

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

1|Updated Mar 12, 2026

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

Ready to run

npx skills add https://github.com/yf8578/clawomics --skill reactome-database-yf8578

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/yf8578/clawomics/tree/main/skills/reactome-database
Command: npx skills add https://github.com/yf8578/clawomics --skill reactome-database-yf8578

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill simplifies the process of querying and analyzing biological pathway data, enabling researchers to understand complex biological processes and gene functions.

Core Features & Use Cases

Pathway Enrichment Analysis: Identify significant biological pathways from gene lists.
Gene-Pathway Mapping: Discover pathways associated with specific genes or proteins.
Data Retrieval: Access detailed information about pathways, reactions, and molecular entities.
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 significantly affected.

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 affected biological pathways from gene lists. This Skill queries the Reactome REST API to map your differentially expressed genes and retrieve curated pathway information programmatically.

What is gene-pathway mapping and how does it help systems biology research?▼

Gene-pathway mapping discovers biological pathways associated with specific genes or proteins. It supports systems biology research by providing programmatic access to curated molecular interactions and reaction data for understanding complex biological processes.

Can I use Python to retrieve molecular interaction data from the Reactome database?▼

Yes, you can retrieve molecular interaction data using Python. This Skill integrates with Python workflows via the reactome2py dependency to seamlessly query the Reactome REST API for detailed pathway and reaction data.

Does this Skill require local installation of the Reactome database to query pathways?▼

No local database installation is required to query pathways. This Skill accesses curated pathway information remotely by querying the Reactome REST API directly, relying only on the requests and reactome2py Python dependencies.

What's the best way to access detailed information about reactions and molecular entities for pathway analysis?▼

The best way to access detailed reaction and molecular entity data is through the Reactome REST API. This Skill provides programmatic access to retrieve comprehensive pathway analysis data and molecular interactions directly into your Python environment.