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Flexible network reconstruction from relational databases with Cytoscape and CytoSQL

Kris Laukens, Jens Hollunder (UGent) , Thanh Hai Dang, Geert De Jaeger (UGent) , Martin Kuiper, Erwin Witters, Alain Verschoren and Koenraad Van Leemput
(2010) BMC BIOINFORMATICS. 11.
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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.
Keywords
WAREHOUSE, PLUGIN, BIOLOGICAL NETWORKS, BIOINFORMATICS

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MLA
Laukens, Kris, et al. “Flexible Network Reconstruction from Relational Databases with Cytoscape and CytoSQL.” BMC BIOINFORMATICS, vol. 11, 2010, doi:10.1186/1471-2105-11-360.
APA
Laukens, K., Hollunder, J., Dang, T. H., De Jaeger, G., Kuiper, M., Witters, E., … Van Leemput, K. (2010). Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. BMC BIOINFORMATICS, 11. https://doi.org/10.1186/1471-2105-11-360
Chicago author-date
Laukens, Kris, Jens Hollunder, Thanh Hai Dang, Geert De Jaeger, Martin Kuiper, Erwin Witters, Alain Verschoren, and Koenraad Van Leemput. 2010. “Flexible Network Reconstruction from Relational Databases with Cytoscape and CytoSQL.” BMC BIOINFORMATICS 11. https://doi.org/10.1186/1471-2105-11-360.
Chicago author-date (all authors)
Laukens, Kris, Jens Hollunder, Thanh Hai Dang, Geert De Jaeger, Martin Kuiper, Erwin Witters, Alain Verschoren, and Koenraad Van Leemput. 2010. “Flexible Network Reconstruction from Relational Databases with Cytoscape and CytoSQL.” BMC BIOINFORMATICS 11. doi:10.1186/1471-2105-11-360.
Vancouver
1.
Laukens K, Hollunder J, Dang TH, De Jaeger G, Kuiper M, Witters E, et al. Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. BMC BIOINFORMATICS. 2010;11.
IEEE
[1]
K. Laukens et al., “Flexible network reconstruction from relational databases with Cytoscape and CytoSQL,” BMC BIOINFORMATICS, vol. 11, 2010.
@article{1038788,
  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.}},
  articleno    = {{360}},
  author       = {{Laukens, Kris and Hollunder, Jens and Dang, Thanh Hai and De Jaeger, Geert and Kuiper, Martin and Witters, Erwin and Verschoren, Alain and Van Leemput, Koenraad}},
  issn         = {{1471-2105}},
  journal      = {{BMC BIOINFORMATICS}},
  keywords     = {{WAREHOUSE,PLUGIN,BIOLOGICAL NETWORKS,BIOINFORMATICS}},
  language     = {{eng}},
  pages        = {{6}},
  title        = {{Flexible network reconstruction from relational databases with Cytoscape and CytoSQL}},
  url          = {{http://doi.org/10.1186/1471-2105-11-360}},
  volume       = {{11}},
  year         = {{2010}},
}
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