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dc.contributor.authorLaukens, K
dc.contributor.authorHollunder, J
dc.contributor.authorThanh, HD
dc.contributor.authorDe Jaeger, G
dc.contributor.authorKuiper, Martin
dc.contributor.authorWitters, E
dc.contributor.authorVerschoren, A
dc.contributor.authorVan Leemput, K
dc.date.accessioned2015-09-21T11:49:07Z
dc.date.accessioned2015-12-03T10:39:23Z
dc.date.available2015-09-21T11:49:07Z
dc.date.available2015-12-03T10:39:23Z
dc.date.issued2010
dc.identifier.citationBMC Bioinformatics 2010, 11nb_NO
dc.identifier.issn1471-2105
dc.identifier.urihttp://hdl.handle.net/11250/2366661
dc.description.abstractBackground: 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.nb_NO
dc.language.isoengnb_NO
dc.publisherBioMed Centralnb_NO
dc.titleFlexible network reconstruction from relational databases with Cytoscape and CytoSQLnb_NO
dc.typeJournal articlenb_NO
dc.typePeer revieweden_GB
dc.date.updated2015-09-21T11:49:06Z
dc.source.volume11nb_NO
dc.source.journalBMC Bioinformaticsnb_NO
dc.identifier.doi10.1186/1471-2105-11-360
dc.identifier.cristin347315
dc.description.localcode© 2010 Laukens et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.nb_NO


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