title: Customizable views on semantically integrated networks for systems biology.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  The Ondex yeast dataset and the OndexView plug-in for Cytoscape are accessible at http://bsu.ncl.ac.uk/ondexview.
authors.affiliation: School of Computing Science, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, UK.
authors.forename: Jochen
authors.initials: J
authors.lastname: Weile
authors.forename: Matthew
authors.initials: M
authors.lastname: Pocock
authors.forename: Simon J
authors.initials: SJ
authors.lastname: Cockell
authors.forename: Phillip
authors.initials: P
authors.lastname: Lord
authors.forename: James M
authors.initials: JM
authors.lastname: Dewar
authors.forename: Eva-Maria
authors.initials: EM
authors.lastname: Holstein
authors.forename: Darren
authors.initials: D
authors.lastname: Wilkinson
authors.forename: David
authors.initials: D
authors.lastname: Lydall
authors.forename: Jennifer
authors.initials: J
authors.lastname: Hallinan
authors.forename: Anil
authors.initials: A
authors.lastname: Wipat
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D016247:Information Storage and Retrieval / Q000379:methods*; D020407:Internet; D012441:Saccharomyces cerevisiae / Q000235:genetics; D049490:Systems Biology / Q000379:methods*; D016615:Telomere / Q000235:genetics