reactome-database

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

8|Updated Jan 13, 2026

Search Tags:#api #pathway analysis #systems biology #reactome #gene expression #enrichment analysis

Ready to run

npx skills add https://github.com/hxk622/TokenDance --skill reactome-database-hxk622

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/hxk622/TokenDance/tree/main/backend/app/skills/builtin/scientific/database/reactome-database
Command: npx skills add https://github.com/hxk622/TokenDance --skill reactome-database-hxk622

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 complex process of querying biological pathway data and performing enrichment analysis, making systems biology research more accessible.

Core Features & Use Cases

Pathway Analysis: Perform overrepresentation and expression analysis on gene lists.
Data Retrieval: Query specific pathway information, molecular interactions, and gene-pathway mappings.
Use Case: Analyze a list of differentially expressed genes from an RNA-Seq experiment to identify the key biological pathways that are significantly altered in a disease state.

Quick Start

Use the reactome-database skill to perform overrepresentation 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 is performed by submitting your gene list to the Reactome API for overrepresentation analysis. This allows you to identify significantly altered biological pathways by mapping your gene expression data directly to known molecular interactions and pathway mappings.

What is Reactome pathway analysis and how does it work for systems biology research?▼

Reactome pathway analysis queries the Reactome REST API to retrieve biological pathway data and perform enrichment analysis. It works by mapping diverse gene identifiers to specific molecular interactions and pathways, providing visualization URLs to help interpret systems biology research results.

Can I use the reactome2py package to map diverse gene identifier types to molecular interactions?▼

Yes, the reactome2py package supports diverse identifier types for gene-pathway mapping and molecular interaction exploration. It queries the Reactome REST API to retrieve specific pathway information, ensuring your identifiers are correctly mapped for systems biology analysis.

Does this pathway analysis approach support RNA-Seq gene expression data?▼

Yes, you can analyze a list of differentially expressed genes from an RNA-Seq experiment to identify key biological pathways significantly altered in a disease state. The skill handles gene expression data by performing overrepresentation and expression analysis via the Reactome API.

What's the best way to retrieve specific pathway information and visualization URLs?▼

The best way to retrieve pathway information and visualization URLs is by querying the Reactome REST API directly. This skill facilitates data retrieval for specific pathways and automatically provides visualization URLs for your analysis results, streamlining biological pathway exploration.

Do I need the requests library to query the Reactome REST API for gene-pathway mapping?▼

Yes, the requests library is required as a dependency alongside reactome2py to query the Reactome REST API. These dependencies enable the skill to execute biological pathway analysis, retrieve molecular interactions, and perform gene-pathway mapping successfully.