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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.
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
WAREHOUSE, PLUGIN, BIOLOGICAL NETWORKS, BIOINFORMATICS
journal title
BMC BIOINFORMATICS
BMC Bioinformatics
volume
11
article_number
360
pages
6 pages
Web of Science type
Article
Web of Science id
000280334600001
JCR category
MATHEMATICAL & COMPUTATIONAL BIOLOGY
JCR impact factor
3.028 (2010)
JCR rank
4/35 (2010)
JCR quartile
1 (2010)
ISSN
1471-2105
DOI
10.1186/1471-2105-11-360
language
English
UGent publication?
yes
classification
A1
copyright statement
I have retained and own the full copyright for this publication
id
1038788
handle
http://hdl.handle.net/1854/LU-1038788
date created
2010-09-08 19:12:08
date last changed
2012-09-19 14:03:51
@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},
  keyword      = {WAREHOUSE,PLUGIN,BIOLOGICAL NETWORKS,BIOINFORMATICS},
  language     = {eng},
  pages        = {6},
  title        = {Flexible network reconstruction from relational databases with Cytoscape and CytoSQL},
  url          = {http://dx.doi.org/10.1186/1471-2105-11-360},
  volume       = {11},
  year         = {2010},
}

Chicago
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.
APA
Laukens, K., Hollunder, J., Dang, T. H., De Jaeger, G., Kuiper, M., Witters, E., Verschoren, A., et al. (2010). Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. BMC BIOINFORMATICS, 11.
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.
MLA
Laukens, Kris, Jens Hollunder, Thanh Hai Dang, et al. “Flexible Network Reconstruction from Relational Databases with Cytoscape and CytoSQL.” BMC BIOINFORMATICS 11 (2010): n. pag. Print.