Reactome Database — Biological Pathway Queries & Enrichment Analysis

Overview

Reactome is an open-source, curated database of biological pathways and reactions for 16+ species. It provides two REST APIs: the Content Service for querying pathway data, entities, and hierarchy, and the Analysis Service for gene/protein list enrichment and expression data overlay. All endpoints return JSON (default) or other formats and require no authentication.

When to Use

• Querying pathway details by stable ID (e.g., R-HSA-69620 for Cell Cycle)
• Searching for pathways, reactions, or entities by keyword
• Running gene list enrichment analysis (over-representation) against Reactome pathways
• Retrieving pathway hierarchy and containment relationships
• Mapping identifiers across databases (UniProt, Ensembl, NCBI, ChEBI)
• Getting species-specific pathway data (human, mouse, rat, and 13+ other organisms)
• Retrieving analysis results by token for sharing or re-filtering
• Building pathway context for multi-omics integration workflows
• For KEGG metabolic pathways and cross-database ID conversion, use kegg-database instead
• For protein-protein interaction networks, use string-database-ppi instead
• For a Python wrapper with caching, consider reactome2py (pip install reactome2py)