The Phenotype and Genotype Experiment Object Model (PaGE-OM): A Robust Data Structure for Information Related to DNA Variation

被引：11

作者：

Brookes, Anthony J. ^{[1
]}

Lehvaslaiho, Heikki ^{[2
]}

Muilu, Juha ^{[3
]}

Shigemoto, Yasumasa ^{[4
]}

Oroguchi, Takashige ^{[5
]}

Tomiki, Takeshi ^{[6
]}

Mukaiyama, Atsuhiro ^{[7
]}

Konagaya, Akihiko ^{[8
]}

Kojima, Toshio ^{[9
]}

Inoue, Ituro ^{[10
]}

Kuroda, Masako ^{[11
]}

Mizushima, Hiroshi ^{[12
]}

Thorisson, Gudmundur A. ^{[1
]}

Dash, Debasis ^{[13
]}

Rajeevan, Haseena ^{[14
]}

Darlison, Matthew W. ^{[15
]}

Woon, Mark ^{[16
]}

Fredman, David ^{[17
]}

Smith, Albert V. ^{[18
]}

Senger, Martin ^{[19
]}

Naito, Kimitoshi ^{[5
]}

Sugawara, Hideaki ^{[20
,21
]}

机构：

[1] Univ Leicester, Dept Genet, Leicester LE1 7RH, Leics, England

[2] Univ Western Cape, S African Natl Bioinformat Inst, ZA-7535 Bellville, South Africa

[3] Inst Mol Med Finland FIMM, Helsinki, Finland

[4] Fujitsu Ltd, BioIT Business Dev Unit, Tokyo, Japan

[5] Strateg Planning Dept, Japan Biol Informat Consortium, Tokyo, Japan

[6] NEC Soft Ltd, VALWAY Technol Ctr, Tokyo, Japan

[7] AXIOHELIX Co Ltd, Tokyo, Japan

[8] Tokyo Inst Technol, Dept Comp Sci, Tokyo 152, Japan

[9] RIKEN, Adv Comp Sci Dept, Yokohama, Kanagawa, Japan

[10] Tokai Univ, Dept Mol Genet, Isehara, Kanagawa, Japan

[11] Japan Sci & Technol Agcy, Dept Adv Databases, Tokyo, Japan

[12] Tokyo Med & Dent Univ, Informat Ctr Med Sci, Tokyo, Japan

[13] Genom Nanotechnol & Robot Knowledge Ctr Genome In, Inst Genom & Integrat Biol, CSIR, Delhi, India

[14] Yale Univ, Dept Genet, New Haven, CT USA

[15] UCL, CHIME London, London WC1E 6BT, England

[16] Stanford Univ, Dept Genet, Stanford, CA 94305 USA

[17] Univ Bergen, Bergen Ctr Computat Sci, Bergen, Norway

[18] Iceland Heart Assoc, Kopavogur, Iceland

[19] Int Rice Res Inst, Crop Res Informat Lab, Manila 1099, Philippines

[20] Natl Inst Genet, Ctr Informat Biol, Mishima, Shizuoka 411, Japan

[21] Natl Inst Genet, DNA Data Bank Japan, Mishima, Shizuoka 411, Japan

来源：

HUMAN MUTATION | 2009年 / 30卷 / 06期

基金：

日本科学技术振兴机构;

关键词：

bioinformatics; data model; genotype-phenotype; database; PROJECT; POPULATION; GENOMICS; FORMAT;

D O I：

10.1002/humu.20973

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

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. (C) 2009 Wiley-Liss, Inc.

引用

页码：968 / 977

页数：10

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