Flexible network reconstruction from relational databases with Cytoscape and CytoSQL
Laukens, K; Hollunder, J; Thanh, HD; De Jaeger, G; Kuiper, Martin; Witters, E; Verschoren, A; Van Leemput, K
Journal article, Peer reviewed

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Date
2010Metadata
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- Institutt for biologi [2673]
- Publikasjoner fra CRIStin - NTNU [40120]
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.