Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.
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.
Laukens
Kris
K
Department of Mathematics and Computer Science, University of Antwerp, Antwerpen, Belgium. kris.laukens@ua.ac.be
Hollunder
Jens
J
Dang
Thanh Hai
TH
De Jaeger
Geert
G
Kuiper
Martin
M
Witters
Erwin
E
Verschoren
Alain
A
Van Leemput
Koenraad
K
D000818:Animals; D002468:Cell Physiological Phenomena; D030541:Databases, Genetic; D023281:Genomics; D006801:Humans; D011506:Proteins / Q000378:metabolism; D012984:Software
D011506:Proteins