Flexible network reconstruction from relational databases with Cytoscape and CytoSQL

BMC Bioinformatics

Software

Kris Laukens¹  Thanh Hai Dang¹  Koenraad Van Leemput¹  Alain Verschoren¹  Jens Hollunder²  Geert De Jaeger²  Martin Kuiper³  Erwin Witters⁴ 

[1] Department of Mathematics and Computer Science, University of Antwerp, Middelheimlaan 1, B-2020, Antwerpen, Belgium;Department of Plant Systems Biology, Flanders Institute for Biotechnology and Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium;Department of Plant Systems Biology, Flanders Institute for Biotechnology and Department of Molecular Genetics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium;Department of Biology, NTNU, Høgskoleringen 5, N-7491, Trondheim, Norway;Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400, Mol, Belgium;Department of Biology, University of Antwerp, Groenenborgerlaan 171, B-2020, Antwerpen, Belgium;

关键词: Relational Database;    Attribute Table;    Structure Query Language;    Node Attribute;    Bind Variable;   

DOI  :  10.1186/1471-2105-11-360

 received in 2009-09-08, accepted in 2010-07-01,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundMolecular 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.ResultsA 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.ConclusionsCytoSQL 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.

【 授权许可】

CC BY   
© Laukens et al; licensee BioMed Central Ltd. 2010