InterStoreDB: A Generic Integration Resource for Genetic and Genomic Data
Identifieur interne : 000461 ( Main/Curation ); précédent : 000460; suivant : 000462InterStoreDB: A Generic Integration Resource for Genetic and Genomic Data
Auteurs : Christopher G. Love [Australie] ; Ambrose E. Andongabo [Royaume-Uni] ; Jun Wang [Royaume-Uni] ; Pierre W. C. Carion [Royaume-Uni] ; Christopher J. Rawlings [Royaume-Uni] ; Graham J. King [Australie]Source :
- Journal of Integrative Plant Biology [ 1672-9072 ] ; 2012-05.
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Abstract
Associating phenotypic traits and quantitative trait loci (QTL) to causative regions of the underlying genome is a key goal in agricultural research. InterStoreDB is a suite of integrated databases designed to assist in this process. The individual databases are species independent and generic in design, providing access to curated datasets relating to plant populations, phenotypic traits, genetic maps, marker loci and QTL, with links to functional gene annotation and genomic sequence data. Each component database provides access to associated metadata, including data provenance and parameters used in analyses, thus providing users with information to evaluate the relative worth of any associations identified. The databases include CropStoreDB, for management of population, genetic map, QTL and trait measurement data, SeqStoreDB for sequence‐related data and AlignStoreDB, which stores sequence alignment information, and allows navigation between genetic and genomic datasets. Genetic maps are visualized and compared using the CMAP tool, and functional annotation from sequenced genomes is provided via an EnsEMBL‐based genome browser. This framework facilitates navigation of the multiple biological domains involved in genetics and genomics research in a transparent manner within a single portal. We demonstrate the value of InterStoreDB as a tool for Brassica research. InterStoreDB is available from: http://www.interstoredb.org
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DOI: 10.1111/j.1744-7909.2012.01120.x
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Love</name><affiliation wicri:level="1"><country xml:lang="fr">Australie</country><wicri:regionArea>Ludwig Institute for Cancer Research, Centre for Medical Research, Royal Melbourne Hospital, Royal Parade, Parkville, Victoria 3050</wicri:regionArea><wicri:noRegion>Victoria 3050</wicri:noRegion></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Australie</country></affiliation></author><author><name sortKey="Andongabo, Ambrose E" sort="Andongabo, Ambrose E" uniqKey="Andongabo A" first="Ambrose E." last="Andongabo">Ambrose E. Andongabo</name><affiliation wicri:level="1"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Biomathematics and Bioinformatics, Rothamsted Research, Harpenden, Herts AL5 2JQ</wicri:regionArea><wicri:noRegion>Herts AL5 2JQ</wicri:noRegion></affiliation></author><author><name sortKey="Wang, Jun" sort="Wang, Jun" uniqKey="Wang J" first="Jun" last="Wang">Jun Wang</name><affiliation wicri:level="4"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Queen Mary University of London, Charterhouse Square, London EC1M 6BQ</wicri:regionArea><orgName type="university">Université de Londres</orgName><placeName><settlement type="city">Londres</settlement><region type="country">Angleterre</region><region type="région" nuts="1">Grand Londres</region></placeName></affiliation></author><author><name sortKey="Carion, Pierre W C" sort="Carion, Pierre W C" uniqKey="Carion P" first="Pierre W. C." last="Carion">Pierre W. C. Carion</name><affiliation wicri:level="1"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Biomathematics and Bioinformatics, Rothamsted Research, Harpenden, Herts AL5 2JQ</wicri:regionArea><wicri:noRegion>Herts AL5 2JQ</wicri:noRegion></affiliation></author><author><name sortKey="Rawlings, Christopher J" sort="Rawlings, Christopher J" uniqKey="Rawlings C" first="Christopher J." last="Rawlings">Christopher J. Rawlings</name><affiliation wicri:level="1"><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Department of Biomathematics and Bioinformatics, Rothamsted Research, Harpenden, Herts AL5 2JQ</wicri:regionArea><wicri:noRegion>Herts AL5 2JQ</wicri:noRegion></affiliation></author><author><name sortKey="King, Graham J" sort="King, Graham J" uniqKey="King G" first="Graham J." last="King">Graham J. King</name><affiliation wicri:level="1"><country xml:lang="fr">Australie</country><wicri:regionArea>Southern Cross Plant Science, Southern Cross University, P.O. Box 157, Lismore NSW 2480</wicri:regionArea><wicri:noRegion>Lismore NSW 2480</wicri:noRegion></affiliation></author></analytic><monogr></monogr><series><title level="j">Journal of Integrative Plant Biology</title><idno type="ISSN">1672-9072</idno><idno type="eISSN">1744-7909</idno><imprint><publisher>Blackwell Publishing Asia</publisher><pubPlace>Melbourne, Australia</pubPlace><date type="published" when="2012-05">2012-05</date><biblScope unit="volume">54</biblScope><biblScope unit="issue">5</biblScope><biblScope unit="page" from="345">345</biblScope><biblScope unit="page" to="355">355</biblScope></imprint><idno type="ISSN">1672-9072</idno></series><idno type="istex">23BC0C161704752BCADD0B2E19188F4725B74823</idno><idno type="DOI">10.1111/j.1744-7909.2012.01120.x</idno><idno type="ArticleID">JIPB1120</idno></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">1672-9072</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>QTL</term><term>bioinformatics</term><term>databases</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract">Associating phenotypic traits and quantitative trait loci (QTL) to causative regions of the underlying genome is a key goal in agricultural research. InterStoreDB is a suite of integrated databases designed to assist in this process. The individual databases are species independent and generic in design, providing access to curated datasets relating to plant populations, phenotypic traits, genetic maps, marker loci and QTL, with links to functional gene annotation and genomic sequence data. Each component database provides access to associated metadata, including data provenance and parameters used in analyses, thus providing users with information to evaluate the relative worth of any associations identified. The databases include CropStoreDB, for management of population, genetic map, QTL and trait measurement data, SeqStoreDB for sequence‐related data and AlignStoreDB, which stores sequence alignment information, and allows navigation between genetic and genomic datasets. Genetic maps are visualized and compared using the CMAP tool, and functional annotation from sequenced genomes is provided via an EnsEMBL‐based genome browser. This framework facilitates navigation of the multiple biological domains involved in genetics and genomics research in a transparent manner within a single portal. We demonstrate the value of InterStoreDB as a tool for Brassica research. InterStoreDB is available from: http://www.interstoredb.org</div></front></TEI></record>Pour manipuler ce document sous Unix (Dilib)
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