Download Reactome data and code

The whole content of the Reactome can be downloaded as:

• MySQL database dump (To use skypainter you also need this database)

Several narrower datasets and download formats are also available:

• Human protein-protein interaction pairs in tab-delimited format.
• Full list of protein-protein interactions, including non-human species.
• Human protein-protein interaction pairs in PSI-MITAB format.
• Uniprot to pathways plus stable id mappings
• Uniprot to pathways mappings
• Curated and inferred Uniprot to pathways mappings
• Gene association file (GO annotation in Reactome)
• Human reactions in SBML (level 2, version 3) format.
• Events in the BioPAX level 2 format
• Events in the BioPAX level 3 format
• Reactome Pathways Gene Set
• Protégé 2.0 ontology for Reactome data model: pins file, pont file, pprj file
• Human pathway diagrams: PDF, or PNG

The complete Reactome textbook of biological pathways and processes can be downloaded in:

• PDF format (ZIP archive).
• RTF format (ZIP archive, split into files on a per-chapter basis).

The Reactome website can be installed locally:

• Instructions for local installation of Reactome database and website.
• Download Reactome website contents and perl code (requires additional non-Reactome software).

Two Java tools are available for Reactome data entry. The Author tool is designed for biologists to input data into Reactome, while the Curator tool is meant for use by curators to annotate biological pathways based on the Reactome schema. N.B. these tools will only wor with a database using our internal database format, the database available from this web page will not work with them. Click on the help link at the top of this page to request a copy of our internal database.

• Curator Tool (version 3.1, build 68, May 11, 2012)
• Author Tool Version 4.0 in Java Web Start
• Author Tool Version 4.0 in Java Applet
• Author Tool (version 2.1, build 25, for some old projects)

A list of functional interactionos (FIs) can be downloaded in three formats. For details about FIs, please see Wu G, Feng X, Stein L.

• MySQL database dump
• Tab delimited text files
• PSI-MITAB format

A SOAP based Web Services API is available to access the Reactome data. For details about this API, please follow the following links:

• Simple Description for the Reactome Web Services API
• Training Materials for the Reactome Web Services API
• Reactome SOAP WS User's Guide in PDF (1M)
• Reactome SOAP WS Tutorial in Power Point Slides (2M)
• Reactome SOAP WS Tutorial in Flash Movie (640 x 480) (11M)
• Reactome SOAP WS Tutorial in Flash Movie (800 x 600) (12M)
• XML Schema for the data model
• WSDL file for the Reactome Web Servies API

A RESTful API (beta) is available too to access the Reactome data. For details about this API, please see this document: Reactome RESTful API