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reactome-database

Query Reactome pathways and perform enrichment analyses via REST APIs.

6|Updated Dec 30, 2025
Search Tags:#python#bioinformatics#enrichment#rest-api#reactome#pathway-analysis#gene-pathway-mapping
One-click install
npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill reactome-database-pur3v4d3r
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/pur3v4d3r/pur3-pkb-codebase/tree/main/.claude/skills/__scientific-skills/reactome-database
Command: npx skills add https://github.com/pur3v4d3r/pur3-pkb-codebase --skill reactome-database-pur3v4d3r

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Reactome provides rich, curated pathway data and analysis services, but researchers often struggle to access data, perform pathway enrichment, and map genes to pathways across multiple tools. This skill centralizes those tasks via REST APIs and a Python client, streamlining biological pathway discovery.

Core Features & Use Cases

  • Content Service access for pathway data, entities, and pathway hierarchies.
  • Analysis Service access for overrepresentation and expression analyses.
  • Reactome2py Python package for easier scripting and automation.
  • Guidance for querying, mapping, and visualizing results in the Pathway Browser.

Quick Start

Pass a list of gene symbols to analyze for enriched Reactome pathways and return top 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 on a list of gene symbols?▼

Pathway enrichment analysis maps a list of gene symbols to Reactome pathways via the Analysis Service REST endpoint, identifying overrepresented pathways and returning top ranked results for biological discovery.

What is gene to pathway mapping and how does it work with Reactome?▼

Gene to pathway mapping connects your identifiers to curated biological pathways using the Reactome Content Service REST endpoint, querying pathway hierarchies and entities to visualize interactions within the Pathway Browser.

Can I automate Reactome REST API queries using Python?▼

You can automate Reactome REST API queries using Python by utilizing the provided scripts and the Reactome2py package, which streamlines Content Service and Analysis Service HTTP requests for batch processing and workflow integration.

Do I need the requests library to use this pathway analysis tool?▼

The requests library is required as a dependency to execute the Python scripts that interface with the Reactome Content Service and Analysis Service REST endpoints for pathway data retrieval and enrichment analysis.

What is the best way to analyze gene lists for enriched pathways across multiple tools?▼

The best way to analyze gene lists for enriched pathways is to centralize the task via REST APIs and Python tooling, streamlining biological pathway discovery by standardizing queries across Reactome Content and Analysis Services.

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