Metazen – metadata capture for metagenomes
Identifieur interne : 000199 ( Main/Merge ); précédent : 000198; suivant : 000200Metazen – metadata capture for metagenomes
Auteurs : Jared Bischof [États-Unis] ; Travis Harrison [États-Unis] ; Tobias Paczian [États-Unis] ; Elizabeth Glass [États-Unis] ; Andreas Wilke [États-Unis] ; Folker Meyer [États-Unis]Source :
- Standards in Genomic Sciences [ 1944-3277 ] ; 2014.
Abstract
As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution.
Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. Unfortunately, these tools are not specifically designed for metagenomic surveys; in particular, they lack the appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools.
Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata.
Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility.
Url:
DOI: 10.1186/1944-3277-9-18
PubMed: 25780508
PubMed Central: 4334943
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PMC:4334943Le document en format XML
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Cass Ave, Argonne, IL 60439, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Glass, Elizabeth" sort="Glass, Elizabeth" uniqKey="Glass E" first="Elizabeth" last="Glass">Elizabeth Glass</name><affiliation wicri:level="2"><nlm:aff id="I1">Computation Institute, University of Chicago, 5735 S Ellis Ave, Chicago, IL 60637, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computation Institute, University of Chicago, 5735 S Ellis Ave, Chicago, IL 60637</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Biological Sciences Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Argonne National Laboratory, 9700 S. 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Cass Ave, Argonne, IL 60439</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Biological Sciences Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author><author><name sortKey="Meyer, Folker" sort="Meyer, Folker" uniqKey="Meyer F" first="Folker" last="Meyer">Folker Meyer</name><affiliation wicri:level="2"><nlm:aff id="I1">Computation Institute, University of Chicago, 5735 S Ellis Ave, Chicago, IL 60637, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Computation Institute, University of Chicago, 5735 S Ellis Ave, Chicago, IL 60637</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Mathematics and Computer Science Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Biological Sciences Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Biological Sciences Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439</wicri:regionArea><placeName><region type="state">Illinois</region></placeName></affiliation></author></analytic><series><title level="j">Standards in Genomic Sciences</title><idno type="eISSN">1944-3277</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>As the impact and prevalence of large-scale metagenomic surveys grow, so does the acute need for more complete and standards compliant metadata. Metadata (data describing data) provides an essential complement to experimental data, helping to answer questions about its source, mode of collection, and reliability. Metadata collection and interpretation have become vital to the genomics and metagenomics communities, but considerable challenges remain, including exchange, curation, and distribution.</p><p>Currently, tools are available for capturing basic field metadata during sampling, and for storing, updating and viewing it. Unfortunately, these tools are not specifically designed for metagenomic surveys; in particular, they lack the appropriate metadata collection templates, a centralized storage repository, and a unique ID linking system that can be used to easily port complete and compatible metagenomic metadata into widely used assembly and sequence analysis tools.</p></sec><sec><title>Results</title><p>Metazen was developed as a comprehensive framework designed to enable metadata capture for metagenomic sequencing projects. Specifically, Metazen provides a rapid, easy-to-use portal to encourage early deposition of project and sample metadata.</p></sec><sec><title>Conclusions</title><p>Metazen is an interactive tool that aids users in recording their metadata in a complete and valid format. A defined set of mandatory fields captures vital information, while the option to add fields provides flexibility.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Field, D" uniqKey="Field D">D Field</name></author><author><name sortKey="Garrity, G" uniqKey="Garrity G">G Garrity</name></author><author><name sortKey="Gray, T" uniqKey="Gray T">T Gray</name></author><author><name sortKey="Morrison, N" uniqKey="Morrison N">N Morrison</name></author><author><name sortKey="Selengut, J" uniqKey="Selengut J">J Selengut</name></author><author><name sortKey="Sterk, P" uniqKey="Sterk P">P Sterk</name></author><author><name sortKey="Tatusova, T" uniqKey="Tatusova T">T Tatusova</name></author><author><name sortKey="Thomson, N" uniqKey="Thomson N">N Thomson</name></author><author><name sortKey="Allen, Mj" uniqKey="Allen M">MJ Allen</name></author><author><name sortKey="Angiuoli, Sv" uniqKey="Angiuoli S">SV 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sortKey="Sklyar, N" uniqKey="Sklyar N">N Sklyar</name></author><author><name sortKey="Taylor, C" uniqKey="Taylor C">C Taylor</name></author><author><name sortKey="Begley, K" uniqKey="Begley K">K Begley</name></author><author><name sortKey="Field, D" uniqKey="Field D">D Field</name></author><author><name sortKey="Harris, S" uniqKey="Harris S">S Harris</name></author><author><name sortKey="Hide, W" uniqKey="Hide W">W Hide</name></author><author><name sortKey="Hofmann, O" uniqKey="Hofmann O">O Hofmann</name></author><author><name sortKey="Neumann, S" uniqKey="Neumann S">S Neumann</name></author><author><name sortKey="Sterk, P" uniqKey="Sterk P">P Sterk</name></author><author><name sortKey="Tong, W" uniqKey="Tong W">W Tong</name></author><author><name sortKey="Sansone, Sa" uniqKey="Sansone S">SA Sansone</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI></record>Pour 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