Observ‐OM and Observ‐TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information
Identifieur interne : 001391 ( Main/Exploration ); précédent : 001390; suivant : 001392Observ‐OM and Observ‐TAB: Universal syntax solutions for the integration, search, and exchange of phenotype and genotype information
Auteurs : Tomasz Adamusiak [Royaume-Uni] ; Helen Parkinson [Royaume-Uni] ; Juha Muilu [Finlande] ; Erik Roos [Pays-Bas] ; Kasper Joeri Van Der Velde [Pays-Bas] ; Gudmundur A. Thorisson [Royaume-Uni] ; Myles Byrne [Finlande] ; Chao Pang [Pays-Bas] ; Sirisha Gollapudi [Royaume-Uni] ; Vincent Ferretti [Canada] ; Hans Hillege [Pays-Bas] ; Anthony J. Brookes [Royaume-Uni] ; Morris A. Swertz [Royaume-Uni, Finlande, Pays-Bas]Source :
- Human Mutation [ 1059-7794 ] ; 2012-05.
English descriptors
- KwdEn :
Abstract
Genetic and epidemiological research increasingly employs large collections of phenotypic and molecular observation data from high quality human and model organism samples. Standardization efforts have produced a few simple formats for exchange of these various data, but a lightweight and convenient data representation scheme for all data modalities does not exist, hindering successful data integration, such as assignment of mouse models to orphan diseases and phenotypic clustering for pathways. We report a unified system to integrate and compare observation data across experimental projects, disease databases, and clinical biobanks. The core object model (Observ‐OM) comprises only four basic concepts to represent any kind of observation: Targets, Features, Protocols (and their Applications), and Values. An easy‐to‐use file format (Observ‐TAB) employs Excel to represent individual and aggregate data in straightforward spreadsheets. The systems have been tested successfully on human biobank, genome‐wide association studies, quantitative trait loci, model organism, and patient registry data using the MOLGENIS platform to quickly setup custom data portals. Our system will dramatically lower the barrier for future data sharing and facilitate integrated search across panels and species. All models, formats, documentation, and software are available for free and open source (LGPLv3) at http://www.observ‐om.org. Hum Mutat 33:867–873, 2012. © 2012 Wiley Periodicals, Inc.
Url:
DOI: 10.1002/humu.22070
Affiliations:
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Box 30001, 9700 RB Groningen</wicri:regionArea><wicri:noRegion>9700 RB Groningen</wicri:noRegion></affiliation></author></analytic><monogr></monogr><series><title level="j">Human Mutation</title><title level="j" type="abbrev">Hum. 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Standardization efforts have produced a few simple formats for exchange of these various data, but a lightweight and convenient data representation scheme for all data modalities does not exist, hindering successful data integration, such as assignment of mouse models to orphan diseases and phenotypic clustering for pathways. We report a unified system to integrate and compare observation data across experimental projects, disease databases, and clinical biobanks. The core object model (Observ‐OM) comprises only four basic concepts to represent any kind of observation: Targets, Features, Protocols (and their Applications), and Values. An easy‐to‐use file format (Observ‐TAB) employs Excel to represent individual and aggregate data in straightforward spreadsheets. The systems have been tested successfully on human biobank, genome‐wide association studies, quantitative trait loci, model organism, and patient registry data using the MOLGENIS platform to quickly setup custom data portals. Our system will dramatically lower the barrier for future data sharing and facilitate integrated search across panels and species. All models, formats, documentation, and software are available for free and open source (LGPLv3) at http://www.observ‐om.org. Hum Mutat 33:867–873, 2012. © 2012 Wiley Periodicals, Inc.</div></front></TEI><affiliations><list><country><li>Canada</li><li>Finlande</li><li>Pays-Bas</li><li>Royaume-Uni</li></country><region><li>Groningue (province)</li><li>Gueldre</li></region><settlement><li>Groningue</li><li>Nimègue</li></settlement></list><tree><country name="Royaume-Uni"><noRegion><name sortKey="Adamusiak, Tomasz" sort="Adamusiak, Tomasz" uniqKey="Adamusiak T" first="Tomasz" last="Adamusiak">Tomasz Adamusiak</name></noRegion><name sortKey="Brookes, Anthony J" sort="Brookes, Anthony J" uniqKey="Brookes A" first="Anthony J." last="Brookes">Anthony J. Brookes</name><name sortKey="Gollapudi, Sirisha" sort="Gollapudi, Sirisha" uniqKey="Gollapudi S" first="Sirisha" last="Gollapudi">Sirisha Gollapudi</name><name sortKey="Parkinson, Helen" sort="Parkinson, Helen" uniqKey="Parkinson H" first="Helen" last="Parkinson">Helen Parkinson</name><name sortKey="Swertz, Morris A" sort="Swertz, Morris A" uniqKey="Swertz M" first="Morris A." last="Swertz">Morris A. Swertz</name><name sortKey="Thorisson, Gudmundur A" sort="Thorisson, Gudmundur A" uniqKey="Thorisson G" first="Gudmundur A." last="Thorisson">Gudmundur A. Thorisson</name></country><country name="Finlande"><noRegion><name sortKey="Muilu, Juha" sort="Muilu, Juha" uniqKey="Muilu J" first="Juha" last="Muilu">Juha Muilu</name></noRegion><name sortKey="Byrne, Myles" sort="Byrne, Myles" uniqKey="Byrne M" first="Myles" last="Byrne">Myles Byrne</name><name sortKey="Muilu, Juha" sort="Muilu, Juha" uniqKey="Muilu J" first="Juha" last="Muilu">Juha Muilu</name><name sortKey="Swertz, Morris A" sort="Swertz, Morris A" uniqKey="Swertz M" first="Morris A." last="Swertz">Morris A. Swertz</name></country><country name="Pays-Bas"><region name="Groningue (province)"><name sortKey="Roos, Erik" sort="Roos, Erik" uniqKey="Roos E" first="Erik" last="Roos">Erik Roos</name></region><name sortKey="Hillege, Hans" sort="Hillege, Hans" uniqKey="Hillege H" first="Hans" last="Hillege">Hans Hillege</name><name sortKey="Pang, Chao" sort="Pang, Chao" uniqKey="Pang C" first="Chao" last="Pang">Chao Pang</name><name sortKey="Swertz, Morris A" sort="Swertz, Morris A" uniqKey="Swertz M" first="Morris A." last="Swertz">Morris A. Swertz</name><name sortKey="Swertz, Morris A" sort="Swertz, Morris A" uniqKey="Swertz M" first="Morris A." last="Swertz">Morris A. Swertz</name><name sortKey="Swertz, Morris A" sort="Swertz, Morris A" uniqKey="Swertz M" first="Morris A." last="Swertz">Morris A. Swertz</name><name sortKey="Van Der Velde, Kasper Joeri" sort="Van Der Velde, Kasper Joeri" uniqKey="Van Der Velde K" first="Kasper Joeri" last="Van Der Velde">Kasper Joeri Van Der Velde</name></country><country name="Canada"><noRegion><name sortKey="Ferretti, Vincent" sort="Ferretti, Vincent" uniqKey="Ferretti V" first="Vincent" last="Ferretti">Vincent Ferretti</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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