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CHENyiru3
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reactome-database

Identify Reactome pathways from gene identifiers via the Analysis Service.

Updated Apr 19, 2026
Search Tags:#api#bioinformatics#token#enrichment#reactome#pathway-analysis#genelist
One-click install
npx skills add https://github.com/CHENyiru3/AI-Skills-Collections --skill reactome-database-chenyiru3
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/CHENyiru3/AI-Skills-Collections/tree/main/skills-market/compbio/databases/reactome
Command: npx skills add https://github.com/CHENyiru3/AI-Skills-Collections --skill reactome-database-chenyiru3

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Reactome provides programmatic access to rest APIs for pathway data, enabling researchers to fetch pathway metadata, map genes to pathways, and perform enrichment analyses in automated workflows.

Core Features & Use Cases

  • Retrieve pathway metadata and participating molecules via the Content Service.
  • Run enrichment analyses against gene lists using the Analysis Service with token-based result retrieval.
  • Use the included Python helper to query, analyze, and orchestrate Reactome data in pipelines.

Quick Start

Provide a gene list file and run an enrichment analysis to retrieve Reactome pathways.

Frequently Asked Questions about reactome-database

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

FAQPage Schema
How do I run Reactome pathway enrichment analysis on a gene list in Python?▼

To run Reactome pathway enrichment analysis, submit a list of gene identifiers to the Analysis Service, then use the token-based mechanism to fetch and view the resulting pathway data.

What is the token-based mechanism used for in Reactome API analysis?▼

The token-based mechanism in Reactome API analysis stores your submitted gene list results, allowing you to fetch and view enrichment analysis pathways at a later time without resubmitting data.

Can I query Reactome Content Service to retrieve pathway metadata and participating molecules?▼

Yes, you can query the Reactome Content Service to retrieve detailed pathway metadata and identify the specific participating molecules involved in those biological pathways.

Does the Reactome Analysis Service support projecting non-human genes to human pathways?▼

Yes, the Reactome Analysis Service supports projecting non-human genes to human pathways, allowing researchers to map gene identifiers from other species onto the human pathway framework.

What dependencies do I need to query Reactome APIs and analyze gene lists?▼

You need the Python requests library installed to query Reactome APIs and analyze gene lists, as it handles the HTTP requests required for both the Content and Analysis Services.

Why use the Reactome API for pathway analysis instead of other bioinformatics enrichment tools?▼

Using the Reactome API for pathway analysis enables automated workflows to fetch pathway metadata, map genes to pathways, and perform enrichment analyses programmatically via REST APIs.

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