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.
• 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 1) format.
• Events in the BioPAX level 2 format
• Events in the BioPAX level 3 format

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. Please note that you need to have root privileges on the computer onto which you plan to install the copy of Reactome.
• 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.

• Author Tool (version 2.1, build 25, September 29, 2006)
• Curator Tool (version 2.1, build 43, November 8, 2008)
• Author Tool Version 3.0 in Java Web Start
• Curator Tool Pre-release in Java Web Start
• Author Tool Version 4.0 Pre-release in Java Web Start
• Author Tool Version 4.0 Pre-release in Java Applet
• Visualization Tool in Java Web Start

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
• User's Guide in PDF (2.3M)
• Tutorial in Power Point Slides (2M)
• Tutorial in Flash Movie (640 x 480) (11M)
• Tutorial in Flash Movie (800 x 600) (12M)
• XML Schema for the data model
• WSDL file for the Reactome Web Servies API