reactome-database
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-databaseinstead - For protein-protein interaction networks, use
string-database-ppiinstead - For a Python wrapper with caching, consider
reactome2py(pip install reactome2py)
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