Customizable views on semantically integrated networks for systems biology

Jochen Weile, Matthew Pocock, Simon J. Cockell, Phillip Lord, James M. Dewar, Eva Maria Holstein, Darren Wilkinson, David Lydall, Jennifer Hallinan, Anil Wipat*

*Corresponding author for this work

Research output: Contribution to journalArticle

5 Citations (Scopus)
6 Downloads (Pure)

Abstract

Motivation: The rise of high-throughput technologies in the post-genomic era has led to the production of large amounts of biological data. Many of these datasets are freely available on the Internet. Making optimal use of these data is a significant challenge for bioinformaticians. Various strategies for integrating data have been proposed to address this challenge. One of the most promising approaches is the development of semantically rich integrated datasets. Although well suited to computational manipulation, such integrated datasets are typically too large and complex for easy visualization and interactive exploration. Results: We have created an integrated dataset for Saccharomyces cerevisiae using the semantic data integration tool Ondex, and have developed a view-based visualization technique that allows for concise graphical representations of the integrated data. The technique was implemented in a plug-in for Cytoscape, called OndexView. We used OndexView to investigate telomere maintenance in S. cerevisiae.

Original languageEnglish
Article numberbtr134
Pages (from-to)1299-1306
Number of pages8
JournalBioinformatics
Volume27
Issue number9
DOIs
Publication statusPublished - May 2011
Externally publishedYes

Bibliographical note

Copyright the Author(s) 2011. Version archived for private and non-commercial use with the permission of the author/s and according to publisher conditions. For further rights please contact the publisher.

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  • Cite this

    Weile, J., Pocock, M., Cockell, S. J., Lord, P., Dewar, J. M., Holstein, E. M., ... Wipat, A. (2011). Customizable views on semantically integrated networks for systems biology. Bioinformatics, 27(9), 1299-1306. [btr134]. https://doi.org/10.1093/bioinformatics/btr134