skills.rest
LeonChaoX
LeonChaoXCOMMUNITY
Explore all skills by this author →
GitHub

reactome-database

Run Reactome pathway enrichment and entity lookups via REST services.

783|65|Updated Feb 27, 2026
Search Tags:#gene mapping#systems biology#rest api#pathway enrichment#reactome#expression analysis
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill reactome-database-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/12-%E7%A7%91%E5%AD%A6%E6%95%B0%E6%8D%AE%E5%BA%93/reactome-database
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill reactome-database-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill helps you turn lists of genes or expression data into biological insight by retrieving Reactome pathway knowledge and running pathway enrichment via Reactome’s REST services.

Core Features & Use Cases

  • Pathway & entity querying: Look up Reactome pathways by stable IDs and fetch participating physical entities, reactions, and related data for systems biology workflows.
  • Pathway enrichment (overrepresentation): Submit gene/protein identifier lists to find statistically enriched pathways, with p-values and FDR.
  • Expression dataset analysis: Analyze TSV expression inputs (with a header starting with #) to identify relevant pathways and generate browser links using analysis tokens.
  • Gene-to-pathway mapping & species projection: Map identifiers to human pathways using the projection endpoint for cross-species studies.

Quick Start

Ask the AI to perform Reactome overrepresentation analysis for your gene list file and return the top enriched pathways with their p-values and FDR.

Frequently Asked Questions about reactome-database

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

FAQPage Schema
How do I perform Reactome pathway enrichment for a gene list?▼

Pathway enrichment for gene lists is performed by submitting identifiers to the Reactome AnalysisService REST endpoint, which returns statistically enriched pathways with p-values and FDR.

What is overrepresentation analysis and when do I need it for systems biology?▼

Overrepresentation analysis identifies if specific biological pathways are statistically enriched in your gene list, helping you understand underlying systems biology mechanisms from expression datasets.

Can I analyze TSV expression datasets with the Reactome API?▼

Yes, you can analyze TSV expression inputs with the Reactome AnalysisService by formatting headers starting with #, generating analysis tokens to retrieve relevant pathways and visualization browser links.

How do I map cross-species gene identifiers to human pathways in Reactome?▼

Use the Reactome projection endpoint to map identifiers from other species to human pathways, enabling cross-species studies and gene-to-pathway mapping through the ContentService REST API.

Do I need specific identifier formats for Reactome ContentService lookups?▼

Yes, Reactome ContentService and AnalysisService REST endpoints require supported identifier formats and TSV or plain-text input rules to successfully fetch physical entities, reactions, and pathway data.

Related Skills

Explore More Education & Research Skills→
ovachieverovachiever
52

reactome-database

Query Reactome REST APIs for pathway retrieval and enrichment analyses.

Community
Intermediate
yf8578yf8578
1

query-reactome

Query Reactome ContentService and AnalysisService APIs for pathway and gene information.

Community
Intermediate
Imad-OuteImad-Oute

reactome-database

Query Reactome pathways and perform enrichment analysis via REST API.

Community
Intermediate
outcomeengoutcomeeng
1

testing

Enforces staged, evidence-first testing workflows prioritizing real dependencies over mocks.

Official
Advanced