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.
Please contact the Reactome This email address is being protected from spambots. You need JavaScript enabled to view it. if you have questions about the files.
Services and Repositories
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Database
Reactome Knowledge GraphFor 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. |
MySQL dumps of Reactome database |
Mapping Files
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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.
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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
- Reactome to OMIM
- Protein Role Reaction
- Disease Variant EWAS mapping file (Read more about our disease variant annotations here).
Icons
The icon mapping files link the source database identifier to elements of the icon library. This folder contains a number of different mapping files to reflect the different source databases.
Complexes
Reactome External Identifiers
Pathway Information
Pathway InformationThese files describe the Reactome pathway hierarchy |
Pathway Diagrams & Figures |
Gene Ontology Association FilesRead more about our GO-CAM project here |
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Systems Biology FormatsHuman reactions in SBML (level 3, v1) All Species reactions in SBML (level 3, v1) Events in the BioPAX level 2 format Events in the BioPAX level 3 format Human pathway diagrams in the SBGN format |
Reactome Pathways Gene Set |
Ontology Files |
Protein-Protein Interaction Files
Protein-Protein Interactions derived from Reactome pathwaysInteractions 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. More information PSI-MITAB format interaction files TAB-delimited format interaction files |
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Functional interactions (FIs) derived from Reactome, and other pathway and interaction databasesFor details about FIs, please see Wu G, Feng X, Stein L. To use these FI networks, please try our ReactomeFIViz Cytoscape app. Version 2022 (Constructed with a new random forest classifier. For more information, refer to Illuminating Dark Proteins using Reactome Pathways) Version 2020 (See note below) Note: The number of predicted FIs has dropped about 50% from Version 2019 to Version 2020 most likely because we excluded BioGrid protein-protein interactions collected in iRefIndex. We found an abnormal high odds ratio for mapped worm protein-protein interaction feature from BioGrid, which was much higher than human PPIs (120 vs. 80) and other no-human PPI features. |
Curation Team Software
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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. |
Our textbook of biological pathways and processes
