skills.rest
Hung-3008
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reactome-database

Retrieve Reactome pathway data and enrichment results via REST APIs.

1|Updated Mar 4, 2026
Search Tags:#api#analysis#enrichment#reactome#pathway#gene-mapping
One-click install
npx skills add https://github.com/Hung-3008/agusta --skill reactome-database-hung-3008
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/reactome-database
Command: npx skills add https://github.com/Hung-3008/agusta --skill reactome-database-hung-3008

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Accessing Reactome's curated pathways, enrichments, and gene-to-pathway mappings requires manual API exploration. This skill provides a programmatic interface to the ContentService and AnalysisService endpoints, enabling automated retrieval, analysis, and integration into research workflows.

Core Features & Use Cases

  • Content Service data retrieval for pathways, reactions, and participating molecules
  • Analysis Service enrichment, expression analysis, and species projection
  • Python CLI helper script and references for API usage
  • Use Case: map gene lists to pathways, retrieve detailed pathway info, and visualize results in the Pathway Browser

Quick Start

Run python scripts/reactome_query.py version to check the database version and then run python reactome_query.py query R-HSA-69278 to fetch a pathway.

Frequently Asked Questions about reactome-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I map a list of genes to Reactome pathways programmatically?▼

Gene-to-pathway mapping is performed by submitting gene lists to the AnalysisService endpoints, which returns enrichment results and cross-species pathway projections via a Python client.

How do I retrieve detailed Reactome pathway data using a REST API?▼

Retrieve Reactome pathway data by querying ContentService endpoints with a pathway identifier, such as R-HSA-69278, to fetch details on reactions and participating molecules.

Can I perform enrichment analysis on gene expression data using Reactome?▼

Enrichment analysis is supported through the AnalysisService REST endpoints, enabling expression analysis and species projection directly within automated research workflows.

Do I need any specific Python dependencies to query Reactome pathways?▼

The Python environment requires the requests library to interact with the Reactome REST APIs, utilizing a lightweight CLI helper script that wraps the ContentService and AnalysisService calls.

What is the best way to automate systems biology pathway queries without manual API exploration?▼

Automating systems biology queries requires a programmatic interface wrapping ContentService and AnalysisService endpoints, replacing manual API exploration with a Python CLI helper for data-intensive workflows.

How do I check the current Reactome database version before running an analysis?▼

Check the database version by running the Python CLI helper script with the version command, ensuring your enrichment and pathway retrieval queries target the correct curated data.

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