reactome-database

Topics in the source

• Reactome Database
• Overview
• When to Use This Skill
• Core Capabilities
• 1. Content Service - Data Retrieval
• 2. Analysis Service - Pathway Analysis
• 3. reactome2py Python Package
• Querying Pathway Data

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. 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 Reactome provides two main API services and a Python client library: 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/ContentSer

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