Journal Article

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL

Witters, Erwin, Laukens, Kris, Dang, Thanh Hai, Hollunder, Jens, De Jaeger, Geert, Kuiper, Martin, Verschoren, Alain, Van Leemput, Koenraad

2010

Overview

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 .

• Publisher: BioMed Central,BioMed Central Ltd,BMC
• Subject: Algorithms / Animals / Applications software / Bioinformatics / Biomedical and Life Sciences / Cell Physiological Phenomena / Computational Biology/Bioinformatics / Computer Appl. in Life Sciences / Databases, Genetic / Gene expression / Genomics / Humans / Life Sciences / Microarrays / Online databases / Proteins - metabolism / Software