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The phenotype and genotype experiment object model (PaGE-OM): a robust data structure for information related to DNA variation

By Anthony J. Brookes, Heikki Lehvaslaiho, Juha Muilu, Yasumasa Shigemoto, Takashige Oroguchi, Takeshi Tomiki, Atsuhiro Mukaiyama, Akihiko Konagaya, Toshio Kojima, Ituro Inoue, Masako Kuroda, Hiroshi Mizushima, Gudmundur A. Thorisson, Debasis Dash, Haseena Rajeevan, Matthew W. Darlison, Mark Woon, David Fredman, Albert V. Smith, Martin Senger, Kimitoshi Naito and Hideaki Sugawara

Abstract

Full text of this item is not currently available on the LRA. \ud The definitive version is available at www3.interscience.wiley.com, Doi: 10.1002/humu.20973.Torrents of genotype–phenotype data are being generated, all of which must be captured, processed, integrated, and exploited. To do this optimally requires the use of standard and interoperable ‘‘object models,’’ providing a description of how to partition the total spectrum of information being dealt with into elemental ‘‘objects’’ (such as ‘‘alleles,’’ ‘‘genotypes,’’ ‘‘phenotype values,’’ ‘‘methods’’) with precisely stated logical interrelationships (such as ‘‘A objects are made up from one or more B objects’’). We herein propose the Phenotype and\ud Genotype Experiment Object Model (PaGE-OM; www.pageom. org), which has been tested and implemented in conjunction with several major databases, and approved as a standard by the Object Management Group (OMG). PaGE-OM is open-source, ready for use by the wider community, and can be further developed as needs arise. It will help to improve information management, assist data integration, and simplify the task of informatics resource design and construction for genotype and phenotype data projects

Topics: bioinformatics, data model, genotype-phenotype, database
Publisher: Wiley-Blackwell
Year: 2009
DOI identifier: 10.1002/humu.20973
OAI identifier: oai:lra.le.ac.uk:2381/8029
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