query-reactome

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

1|Updated Mar 12, 2026

Search Tags:#bioinformatics #pathway analysis #reactome #reaction mechanism #gene enrichment #biological pathways

Ready to run

npx skills add https://github.com/yf8578/clawomics --skill query-reactome-yf8578

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: query-reactome
Source: https://github.com/yf8578/clawomics/tree/main/skills/query-reactome
Command: npx skills add https://github.com/yf8578/clawomics --skill query-reactome-yf8578

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill helps researchers and bioinformaticians understand complex biological processes by querying the Reactome database for pathways, reactions, and gene information.

Core Features & Use Cases

Pathway Discovery: Search for biological pathways related to specific keywords (e.g., "DNA repair", "apoptosis").
Detailed Information: Retrieve detailed information about specific pathways, including participants and reaction mechanisms.
Pathway Enrichment: Perform pathway enrichment analysis on a list of genes to identify over-represented biological pathways.
Use Case: A researcher has a list of genes identified in a cancer study and wants to know which biological pathways are most significantly affected. They can use this Skill to perform pathway enrichment analysis.

Quick Start

Use the query-reactome skill to search for pathways related to 'cell cycle'.

Frequently Asked Questions about query-reactome

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 genes?▼

Pathway enrichment analysis on a list of genes is performed by querying the Reactome AnalysisService API to identify over-represented biological pathways. This allows researchers to determine which pathways are significantly affected in their specific study context.

What biological pathway information can I retrieve from the Reactome database?▼

Biological pathway information retrieved from the Reactome database includes pathway details, reaction mechanisms, and pathway participants. Querying the ContentService API allows users to search pathways by keyword and look up specific gene information within Reactome.

Can I search for biological pathways using specific keywords like DNA repair?▼

Searching for biological pathways by specific keywords like DNA repair is supported through the Reactome ContentService API. This returns matching pathways and reaction mechanisms, enabling targeted discovery of molecular processes related to the search terms.

How do I find reaction mechanisms and participants for a specific biological pathway?▼

Finding reaction mechanisms and participants for a specific biological pathway involves fetching detailed pathway information via the Reactome ContentService API. This provides a breakdown of the molecular participants and the specific reactions that constitute the pathway.

What is the best way to query Reactome for gene enrichment and molecular mechanisms?▼

Querying Reactome for gene enrichment and molecular mechanisms is best handled by utilizing the AnalysisService for gene list enrichment and the ContentService for reaction mechanisms. This approach provides comprehensive pathway analysis by leveraging both APIs to map genes to biological processes.