reactome-database

# Reactome Database ## Overview Reactome is a free, open-source, curated pathway database with 2,825+ human pathways. Query biological pathways, perform overrepresentation and expression analysis, map genes to pathways, explore molecular interactions via REST API and Python client for systems biology research. ## When to Use This Skill This skill should be used when: - Performing pathway enrichment analysis on gene or protein lists - Analyzing gene expression data to identify relevant biological pathways - Querying specific pathway information, reactions, or molecular interactions - Mapping genes or proteins to biological pathways and processes - Exploring disease-related pathways and mechanisms - Visualizing analysis results in the Reactome Pathway Browser - Conducting comparative pathway analysis across species ## Core Capabilities Reactome provides two main API services and a Python client library: ### 1. Content Service - Data Retrieval Query and retrieve biological pathway data, molecular interactions, and entity information. **Common operations:** - Retrieve pathway information and hierarchies - Query specific entities (proteins, reactions, complexes) - Get participating molecules in pathways - Access database version and metadata - Explore pathway compartments and locations **API Base URL:** `https://reactome.org/ContentService` ### 2. Analysis Service - Pathway Analysis Perform computational analysis on gene lists and expression data. **Analysis types:** ...