{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T21:54:43Z","timestamp":1761947683062},"reference-count":44,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2027,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: The Ondex yeast dataset and the OndexView plug-in for Cytoscape are accessible at http:\/\/bsu.ncl.ac.uk\/ondexview.<\/jats:p>\n               <jats:p>Contact: \u00a0anil.wipat@ncl.ac.uk<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data is available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr134","type":"journal-article","created":{"date-parts":[[2011,3,18]],"date-time":"2011-03-18T01:09:30Z","timestamp":1300410570000},"page":"1299-1306","source":"Crossref","is-referenced-by-count":5,"title":["Customizable views on semantically integrated networks for systems biology"],"prefix":"10.1093","volume":"27","author":[{"given":"Jochen","family":"Weile","sequence":"first","affiliation":[{"name":"1 School of Computing Science, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, 2Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, 3Centre for Integrative Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, 4School of Mathematics and Statistics, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU and 5Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew","family":"Pocock","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, 2Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, 3Centre for Integrative Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, 4School of Mathematics and Statistics, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU and 5Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simon J.","family":"Cockell","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, 2Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, 3Centre for Integrative Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, 4School of Mathematics and Statistics, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU and 5Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Phillip","family":"Lord","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, 2Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, 3Centre for Integrative Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, 4School of Mathematics and Statistics, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU and 5Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James M.","family":"Dewar","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, 2Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, 3Centre for Integrative Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, 4School of Mathematics and Statistics, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU and 5Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eva\u2212Maria","family":"Holstein","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, 2Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, 3Centre for Integrative Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, 4School of Mathematics and Statistics, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU and 5Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Darren","family":"Wilkinson","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, 2Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, 3Centre for Integrative Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, 4School of Mathematics and Statistics, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU and 5Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK"},{"name":"1 School of Computing Science, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, 2Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, 3Centre for Integrative Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, 4School of Mathematics and Statistics, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU and 5Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Lydall","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, 2Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, 3Centre for Integrative Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, 4School of Mathematics and Statistics, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU and 5Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK"},{"name":"1 School of Computing Science, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, 2Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, 3Centre for Integrative Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, 4School of Mathematics and Statistics, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU and 5Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jennifer","family":"Hallinan","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, 2Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, 3Centre for Integrative Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, 4School of Mathematics and Statistics, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU and 5Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anil","family":"Wipat","sequence":"additional","affiliation":[{"name":"1 School of Computing Science, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, 2Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, 3Centre for Integrative Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, 4School of Mathematics and Statistics, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU and 5Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK"},{"name":"1 School of Computing Science, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, 2Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, 3Centre for Integrative Systems Biology of Ageing and Nutrition, Institute for Ageing and Health, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE4 5PL, 4School of Mathematics and Statistics, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU and 5Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, 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