Reactome provides open-source and open-data. We have continuously supported the major open-data standards, including BioPAX, PSI-MITAB, SBML and SBGN export formats. The Reactome data and source code continue to be publicly accessible under the terms of Creative Commons Licenses. Please refer to our License Agreement.
Graph Database
For more information on the installation of the Reactome Graph Database, please refer to the Get Started section of the Graph Database documentation in the Developer Guide.
Services and GitHub Repository
- Content Service: Our new Content Service provides outside users with direct access to pathway data in Reactome.
- Analysis Service: The Reactome Pathway Analysis Tools are also available for integration into third party websites.
- GitHub Repository
Identifier mapping files
Mapping files link the source database identifier to the lowest level pathway diagram or subset of the pathway, all levels of the pathway hierarchy or database identifier to all reactions. Read more about the format.
- Lowest level pathway diagram / Subset of the pathway
- All levels of the pathway hierarchy
- Database identifier to all reactions
Physical Entity (PE) Identifier mapping files
Mapping files link the source database identifier to the lowest level pathway diagram or subset of the pathway. Read more about the format.
- Lowest level pathway diagram / Subset of the pathway
- All levels of the pathway hierarchy
- Database identifier to all reactions
Other Mappings
- BioModels to Pathways
- Reaction PMIDs - Read more about the format
- Reactome to OMIM - Read more about the format
- Protein Role Reaction - Read more about the format
Pathways
- Pathway Information. Read more about the format
- Pathway Diagrams and Illustrations
Complexes
Reactome External Identifiers
Protein-Protein Interactions derived from Reactome pathways
Interactions are inferred between all protein components of a complex. To limit the creation of false-positive inferences, only complexes with four or fewer protein components are considered.
- PSI-MITAB format interaction files
- TAB-delimited format interaction files
Specialized data formats
- Gene association file (GO annotation in Reactome)
- Human reactions in SBML (level 3, version 1) format
- All Species reactions in SBML (level 3, version 1) format
- Events in the BioPAX level 2 format.
- Events in the BioPAX level 3 format.
- Events in the SBGN format.
- Reactome Pathways Gene Set.
- Protégé 2.0 ontology for Reactome data model: pins file, pont file, pprj file.
Functional interactions (FIs) derived from Reactome, and other pathway and interaction databases
For details about FIs, please see Wu G, Feng X, Stein L. To use these FI networks, please try our ReactomeFIViz Cytoscape app.
MySQL dumps of Reactome databases
- Main database
- Simplified database (deprecated). Please note that this file will no longer be available as of Version 66.
- Stable identifiers database
Curation Software
The Curator tool is meant for use by curators to annotate biological pathways based on the Reactome schema. Please note that this tool will only work with a database using our internal database format; the database available from this web page will not work with them.
Reactome textbook of biological pathways and processes
Note: RTF files may be very large, but conversion to PDF or Word generates a file that is much smaller with no loss of information