Title
Flexible network reconstruction from relational databases with Cytoscape and CytoSQL Flexible network reconstruction from relational databases with Cytoscape and CytoSQL
Author
Faculty/Department
Faculty of Sciences. Biology
Faculty of Sciences. Mathematics and Computer Science
Publication type
article
Publication
London ,
Subject
Biology
Computer. Automation
Source (journal)
BMC bioinformatics. - London
Volume/pages
11(2010) , p. 360,1-360,10
ISSN
1471-2105
ISI
000280334600001
Carrier
E
Target language
English (eng)
Full text (Publishers DOI)
Affiliation
University of Antwerp
Abstract
Background Molecular interaction networks can be efficiently studied using network visualization software such as Cytoscape. The relevant nodes, edges and their attributes can be imported in Cytoscape in various file formats, or directly from external databases through specialized third party plugins. However, molecular data are often stored in relational databases with their own specific structure, for which dedicated plugins do not exist. Therefore, a more generic solution is presented. Results A new Cytoscape plugin 'CytoSQL' is developed to connect Cytoscape to any relational database. It allows to launch SQL ('Structured Query Language') queries from within Cytoscape, with the option to inject node or edge features of an existing network as SQL arguments, and to convert the retrieved data to Cytoscape network components. Supported by a set of case studies we demonstrate the flexibility and the power of the CytoSQL plugin in converting specific data subsets into meaningful network representations. Conclusions CytoSQL offers a unified approach to let Cytoscape interact with relational databases. Thanks to the power of the SQL syntax, this tool can rapidly generate and enrich networks according to very complex criteria. The plugin is available at http://www.ptools.ua.ac.be/CytoSQL.
Full text (open access)
https://repository.uantwerpen.be/docman/irua/3807bc/ac6bc9e6.pdf
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