skills.rest
LogauaEngstrom
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reactome-database

Query Reactome REST APIs for pathways, analyses, and entity mapping.

18|1|Updated Dec 27, 2025
Search Tags:#analysis#bioinformatics#enrichment#rest-api#reactome#gene#pathway
One-click install
npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill reactome-database-logauaengstrom
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/LogauaEngstrom/claude-scientific-skills/tree/main/scientific-skills/reactome-database
Command: npx skills add https://github.com/LogauaEngstrom/claude-scientific-skills --skill reactome-database-logauaengstrom

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Programmatic access to Reactome's REST APIs for retrieving pathways, performing enrichment analyses, and mapping genes to pathways to support systems-biology research workflows.

Core Features & Use Cases

  • Content Service data retrieval (pathways, entities, and hierarchies)
  • Analysis Service enrichment and expression analyses, with token-based results
  • Pathway/entity mapping and browser URL generation for visualization and exploration

Quick Start

Query Reactome data and run pathway analyses from gene lists using REST endpoints and a Python client to retrieve and visualize results.

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 using a gene list?▼

Pathway enrichment analysis is performed by submitting a gene list to the Reactome Analysis Service REST API, then retrieving overrepresentation results using a token-based system. This allows programmatic identification of statistically enriched biological pathways.

Can I retrieve Reactome pathways and hierarchies programmatically?▼

Yes, Reactome pathways, entities, and hierarchies can be retrieved programmatically by querying the Content Service REST API. This enables automated access to systems-biology data for pathway retrieval and species projection across human and model organisms.

What's the best way to map genes to Reactome pathways in Python?▼

Mapping genes to Reactome pathways in Python is best achieved by using the requests library to call Reactome REST endpoints. This handles JSON responses to perform entity mapping and generates browser URLs for data visualization.

Do I need prior REST API knowledge to use Reactome data services?▼

Yes, you need knowledge of REST endpoints, Python requests usage, and JSON response handling to query Reactome data services. This prerequisite knowledge is required to perform analyses, species projection, and token-based result retrieval.

Does this approach support species projection for model organisms?▼

Yes, species projection is supported for both human and model organisms. The Reactome Analysis Service applies REST API queries to project gene lists and pathway data across different species, enabling comparative systems-biology research workflows.

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