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The phenotype and genotype experiment object model (PaGE‐OM): a robust data structure for information related to DNA variation
Author(s) -
Brookes Anthony J.,
Lehvaslaiho Heikki,
Muilu Juha,
Shigemoto Yasumasa,
Oroguchi Takashige,
Tomiki Takeshi,
Mukaiyama Atsuhiro,
Konagaya Akihiko,
Kojima Toshio,
Inoue Ituro,
Kuroda Masako,
Mizushima Hiroshi,
Thorisson Gudmundur A.,
Dash Debasis,
Rajeevan Haseena,
Darlison Matthew W.,
Woon Mark,
Fredman David,
Smith Albert V.,
Senger Martin,
Naito Kimitoshi,
Sugawara Hideaki
Publication year - 2009
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.20973
Subject(s) - phenotype , genotype , biology , partition (number theory) , interoperability , object (grammar) , variation (astronomy) , computer science , computational biology , genetics , gene , artificial intelligence , world wide web , physics , mathematics , combinatorics , astrophysics
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 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.Hum Mutat 30, 968–977, 2009. © 2009 Wiley‐Liss, Inc.