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Flexible network reconstruction from relational databases with Cytoscape and CytoSQL

Kris Laukens1*, Jens Hollunder2, Thanh Hai Dang1, Geert De Jaeger2, Martin Kuiper23, Erwin Witters45, Alain Verschoren1 and Koenraad Van Leemput1

Author Affiliations

1 Department of Mathematics and Computer Science, University of Antwerp, Middelheimlaan 1, B-2020 Antwerpen, Belgium

2 Department of Plant Systems Biology, Flanders Institute for Biotechnology and Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium

3 Department of Biology, NTNU, Høgskoleringen 5, N-7491 Trondheim, Norway

4 Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol, Belgium

5 Department of Biology, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerpen, Belgium

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BMC Bioinformatics 2010, 11:360  doi:10.1186/1471-2105-11-360

Published: 1 July 2010

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 webcite.