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Installing a Local Copy of the Reactome Web Site and Database

Imre Vastrik¹

¹EMBL‐European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, U.K.

Publication Name:

Current Protocols in Bioinformatics

Unit Number:

Unit 9.10

DOI:

10.1002/0471250953.bi0910s21

Online Posting Date:

March, 2008

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Abstract

The Reactome project builds, maintains, and publishes a database of biological pathways. The information in the database is gathered from the experts in the field, peer reviewed, and edited by Reactome editorial staff and then published to the Reactome Web site, http://www.reactome.org (see unit 8.7). Reactome software is open source and builds on top of other open-source or freely available software. Reactome data and code can be freely downloaded in its entirety and the Web site installed locally. This allows for more flexible interrogation of the data and also makes it possible to add one's own information to the database. Curr. Protoc. Bioinform. 21:9.10.1-9.10.9. © 2008 by John Wiley & Sons, Inc.

Keywords: pathways database; open source software

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Introduction
Basic Protocol: Installation of the Reactome Web Site and Data
Installation of Other Applications and Libraries
Support Protocol 1: Installing Apache, Perl, and Java
Support Protocol 2: Installing MySQL
Support Protocol 3: Installing Perl Modules and Supporting Software
Commentary
Figures
Tables

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Figures

Figure 9.10.1

Screenshot of the Web site front page after successful installation of a local copy of the Reactome database and Web site.

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Figure 9.10.2

Architectural diagram of the Reactome software. The information is entered into the database with the help of Reactome Curator Tool. To enable off-line work, the latter can also store information in an XML file in the local file system. End users usually access Reactome database content with a Web browser via the Web server, where the request is handled by the CGI scripts that interrogate the MySQL database via Perl API.

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