Sciweavers

Share
BMCBI
2010

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL

11 years 1 months ago
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 i...
Kris Laukens, Jens Hollunder, Thanh Hai Dang, Geer
Added 08 Dec 2010
Updated 08 Dec 2010
Type Journal
Year 2010
Where BMCBI
Authors Kris Laukens, Jens Hollunder, Thanh Hai Dang, Geert De Jaeger, Martin Kuiper, Erwin Witters, Alain Verschoren, Koenraad Van Leemput
Comments (0)
books