skills.rest
JosephWoodall
JosephWoodallCOMMUNITY
Explore all skills by this author →
𝕏@josephwoodall_GitHub

reactome-database

Query Reactome REST APIs to retrieve pathway data and map genes.

1|Updated Mar 19, 2026
Search Tags:#analysis#bioinformatics#pathways#enrichment#genes#reactome
One-click install
npx skills add https://github.com/JosephWoodall/noosphere --skill reactome-database-josephwoodall
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: reactome-database
Source: https://github.com/JosephWoodall/noosphere/tree/main/.agent/skills/reactome-database
Command: npx skills add https://github.com/JosephWoodall/noosphere --skill reactome-database-josephwoodall

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Researchers need programmatic access to Reactome to fetch pathway data, map genes to pathways, and run analyses for systems biology studies.

Core Features & Use Cases

  • Content Service access: retrieve pathway data, participating entities, and database metadata
  • Analysis Service access: perform pathway enrichment and expression analyses
  • Python client integration: simple CLI script to query, analyze, and explore results

Quick Start

Ask the AI to fetch information for a pathway by ID using the Reactome REST API.

Frequently Asked Questions about reactome-database

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

FAQPage Schema
How do I run pathway enrichment analysis using the Reactome REST API?▼

You can perform pathway enrichment analysis by submitting gene lists to the Reactome Analysis Service, which returns token-based analysis results for systems biology studies. The process streamlines retrieval, mapping, and visualization across species.

What is gene-to-pathway mapping and when do I need it for bioinformatics?▼

Gene-to-pathway mapping connects genes to known biological pathways using database metadata. Researchers need it when fetching pathway data to interpret systems biology results and visualize participating entities across species.

Can I use Python to query Reactome pathway data and handle API rate limits?▼

Yes, you can use a Python client to query Reactome pathway data, integrating careful handling of API endpoints, tokens, rate limits, and error responses for deterministic API usage in bioinformatics workflows.

How do I retrieve pathway data and participating entities by pathway ID?▼

Retrieve pathway data and participating entities by querying the Reactome Content Service with a specific pathway ID. This fetches database metadata and pathway information needed for downstream analysis.

Does the Reactome Analysis Service support expression analysis and visualization across species?▼

Yes, the Reactome Analysis Service supports expression analysis and visualization across species. It streamlines pathway retrieval and analysis results through token-based workflows for bioinformatics researchers.

Related Skills

Explore More Education & Research Skills→
biomaps-infrabiomaps-infra

db-reactome

Query the Reactome REST API for pathway enrichment and gene-pathway mapping.

Official
Intermediate
hxk622hxk622
8

reactome-database

Query the Reactome REST API for pathway enrichment and gene-pathway mapping.

Community
Intermediate
Yezez9Yezez9

reactome-database

Query Reactome REST API for pathway enrichment and gene-pathway mapping.

Community
Intermediate
tassiovaletassiovale
13

pathway-enrichment

Analyze gene lists or ranked data for enriched biological pathways and gene sets.

Community
Advanced