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Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding

Identifieur interne : 000463 ( Ncbi/Merge ); précédent : 000462; suivant : 000464

Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding

Auteurs : Trupti Joshi [États-Unis] ; Michael R. Fitzpatrick [États-Unis] ; Shiyuan Chen [États-Unis] ; Yang Liu [États-Unis] ; Hongxin Zhang [États-Unis] ; Ryan Z. Endacott [États-Unis] ; Eric C. Gaudiello [États-Unis] ; Gary Stacey [États-Unis] ; Henry T. Nguyen [États-Unis] ; Dong Xu [États-Unis]

Source :

RBID : PMC:3965117

Abstract

Soybean Knowledge Base (http://soykb.org) is a comprehensive web resource developed for bridging soybean translational genomics and molecular breeding research. It provides information for six entities including genes/proteins, microRNAs/sRNAs, metabolites, single nucleotide polymorphisms, plant introduction lines and traits. It also incorporates many multi-omics datasets including transcriptomics, proteomics, metabolomics and molecular breeding data, such as quantitative trait loci, traits and germplasm information. Soybean Knowledge Base has a new suite of tools such as In Silico Breeding Program for soybean breeding, which includes a graphical chromosome visualizer for ease of navigation. It integrates quantitative trait loci, traits and germplasm information along with genomic variation data, such as single nucleotide polymorphisms, insertions, deletions and genome-wide association studies data, from multiple soybean cultivars and Glycine soja.


Url:
DOI: 10.1093/nar/gkt905
PubMed: 24136998
PubMed Central: 3965117

Links toward previous steps (curation, corpus...)


Links to Exploration step

PMC:3965117

Le document en format XML

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</affiliation>
<affiliation wicri:level="2">
<nlm:aff id="gkt905-AFF1">Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Division of Plant Sciences, University of Missouri, Columbia, MO 65211</wicri:regionArea>
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<region type="state">Missouri (État)</region>
</placeName>
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</author>
<author>
<name sortKey="Nguyen, Henry T" sort="Nguyen, Henry T" uniqKey="Nguyen H" first="Henry T." last="Nguyen">Henry T. Nguyen</name>
<affiliation wicri:level="2">
<nlm:aff id="gkt905-AFF1">Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA,</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211</wicri:regionArea>
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<region type="state">Missouri (État)</region>
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<nlm:aff id="gkt905-AFF1">National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA,</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211</wicri:regionArea>
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<region type="state">Missouri (État)</region>
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<country xml:lang="fr">États-Unis</country>
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</author>
<author>
<name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name>
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<affiliation wicri:level="2">
<nlm:aff id="gkt905-AFF1">Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA,</nlm:aff>
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<affiliation wicri:level="2">
<nlm:aff id="gkt905-AFF1">National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA,</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211</wicri:regionArea>
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<region type="state">Missouri (État)</region>
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<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Informatics Institute, University of Missouri, Columbia, MO 65211</wicri:regionArea>
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<series>
<title level="j">Nucleic Acids Research</title>
<idno type="ISSN">0305-1048</idno>
<idno type="eISSN">1362-4962</idno>
<imprint>
<date when="2013">2013</date>
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<front>
<div type="abstract" xml:lang="en">
<p>Soybean Knowledge Base (
<ext-link ext-link-type="uri" xlink:href="http://soykb.org">http://soykb.org</ext-link>
) is a comprehensive web resource developed for bridging soybean translational genomics and molecular breeding research. It provides information for six entities including genes/proteins, microRNAs/sRNAs, metabolites, single nucleotide polymorphisms, plant introduction lines and traits. It also incorporates many multi-omics datasets including transcriptomics, proteomics, metabolomics and molecular breeding data, such as quantitative trait loci, traits and germplasm information. Soybean Knowledge Base has a new suite of tools such as
<italic>In Silico</italic>
Breeding Program for soybean breeding, which includes a graphical chromosome visualizer for ease of navigation. It integrates quantitative trait loci, traits and germplasm information along with genomic variation data, such as single nucleotide polymorphisms, insertions, deletions and genome-wide association studies data, from multiple soybean cultivars and
<italic>Glycine soja</italic>
.</p>
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<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id>
<journal-id journal-id-type="iso-abbrev">Nucleic Acids Res</journal-id>
<journal-id journal-id-type="publisher-id">nar</journal-id>
<journal-id journal-id-type="hwp">nar</journal-id>
<journal-title-group>
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<issn pub-type="ppub">0305-1048</issn>
<issn pub-type="epub">1362-4962</issn>
<publisher>
<publisher-name>Oxford University Press</publisher-name>
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</journal-meta>
<article-meta>
<article-id pub-id-type="pmid">24136998</article-id>
<article-id pub-id-type="pmc">3965117</article-id>
<article-id pub-id-type="doi">10.1093/nar/gkt905</article-id>
<article-id pub-id-type="publisher-id">gkt905</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>VII. Plant databases</subject>
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<title-group>
<article-title>Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding</article-title>
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<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Joshi</surname>
<given-names>Trupti</given-names>
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<xref ref-type="aff" rid="gkt905-AFF1">
<sup>1</sup>
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<xref ref-type="aff" rid="gkt905-AFF1">
<sup>2</sup>
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<xref ref-type="aff" rid="gkt905-AFF1">
<sup>3</sup>
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<xref ref-type="aff" rid="gkt905-AFF1">
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<xref ref-type="aff" rid="gkt905-AFF1">
<sup>1</sup>
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<xref ref-type="aff" rid="gkt905-AFF1">
<sup>2</sup>
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</name>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>2</sup>
</xref>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Zhang</surname>
<given-names>Hongxin</given-names>
</name>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Endacott</surname>
<given-names>Ryan Z.</given-names>
</name>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Gaudiello</surname>
<given-names>Eric C.</given-names>
</name>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Stacey</surname>
<given-names>Gary</given-names>
</name>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>2</sup>
</xref>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>3</sup>
</xref>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Nguyen</surname>
<given-names>Henry T.</given-names>
</name>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>2</sup>
</xref>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>3</sup>
</xref>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Xu</surname>
<given-names>Dong</given-names>
</name>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>1</sup>
</xref>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>2</sup>
</xref>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>3</sup>
</xref>
<xref ref-type="aff" rid="gkt905-AFF1">
<sup>4</sup>
</xref>
<xref ref-type="corresp" rid="gkt905-COR1">*</xref>
</contrib>
<aff id="gkt905-AFF1">
<sup>1</sup>
Department of Computer Science, University of Missouri, Columbia, MO 65211, USA,
<sup>2</sup>
Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA,
<sup>3</sup>
National Center for Soybean Biotechnology, University of Missouri, Columbia, MO 65211, USA,
<sup>4</sup>
Informatics Institute, University of Missouri, Columbia, MO 65211, USA and
<sup>5</sup>
Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA</aff>
</contrib-group>
<author-notes>
<corresp id="gkt905-COR1">*To whom correspondence should be addressed. Tel:
<phone>+1 573 882 2299</phone>
; Fax:
<fax>+1 573 882 8318</fax>
; Email:
<email>xudong@missouri.edu</email>
</corresp>
</author-notes>
<pub-date pub-type="ppub">
<day>1</day>
<month>1</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="epub">
<day>9</day>
<month>10</month>
<year>2013</year>
</pub-date>
<pub-date pub-type="pmc-release">
<day>9</day>
<month>10</month>
<year>2013</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the . </pmc-comment>
<volume>42</volume>
<issue>Database issue</issue>
<issue-title>Database issue</issue-title>
<fpage>D1245</fpage>
<lpage>D1252</lpage>
<history>
<date date-type="received">
<day>15</day>
<month>8</month>
<year>2013</year>
</date>
<date date-type="rev-recd">
<day>12</day>
<month>9</month>
<year>2013</year>
</date>
<date date-type="accepted">
<day>16</day>
<month>9</month>
<year>2013</year>
</date>
</history>
<permissions>
<copyright-statement>© The Author(s) 2013. Published by Oxford University Press.</copyright-statement>
<copyright-year>2013</copyright-year>
<license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by/3.0/">
<license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (
<uri xlink:type="simple" xlink:href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</uri>
), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com</license-p>
</license>
</permissions>
<abstract>
<p>Soybean Knowledge Base (
<ext-link ext-link-type="uri" xlink:href="http://soykb.org">http://soykb.org</ext-link>
) is a comprehensive web resource developed for bridging soybean translational genomics and molecular breeding research. It provides information for six entities including genes/proteins, microRNAs/sRNAs, metabolites, single nucleotide polymorphisms, plant introduction lines and traits. It also incorporates many multi-omics datasets including transcriptomics, proteomics, metabolomics and molecular breeding data, such as quantitative trait loci, traits and germplasm information. Soybean Knowledge Base has a new suite of tools such as
<italic>In Silico</italic>
Breeding Program for soybean breeding, which includes a graphical chromosome visualizer for ease of navigation. It integrates quantitative trait loci, traits and germplasm information along with genomic variation data, such as single nucleotide polymorphisms, insertions, deletions and genome-wide association studies data, from multiple soybean cultivars and
<italic>Glycine soja</italic>
.</p>
</abstract>
<counts>
<page-count count="8"></page-count>
</counts>
<custom-meta-group>
<custom-meta>
<meta-name>cover-date</meta-name>
<meta-value>1 January 2014</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
</front>
</pmc>
<affiliations>
<list>
<country>
<li>États-Unis</li>
</country>
<region>
<li>Missouri (État)</li>
</region>
</list>
<tree>
<country name="États-Unis">
<region name="Missouri (État)">
<name sortKey="Joshi, Trupti" sort="Joshi, Trupti" uniqKey="Joshi T" first="Trupti" last="Joshi">Trupti Joshi</name>
</region>
<name sortKey="Chen, Shiyuan" sort="Chen, Shiyuan" uniqKey="Chen S" first="Shiyuan" last="Chen">Shiyuan Chen</name>
<name sortKey="Chen, Shiyuan" sort="Chen, Shiyuan" uniqKey="Chen S" first="Shiyuan" last="Chen">Shiyuan Chen</name>
<name sortKey="Endacott, Ryan Z" sort="Endacott, Ryan Z" uniqKey="Endacott R" first="Ryan Z." last="Endacott">Ryan Z. Endacott</name>
<name sortKey="Endacott, Ryan Z" sort="Endacott, Ryan Z" uniqKey="Endacott R" first="Ryan Z." last="Endacott">Ryan Z. Endacott</name>
<name sortKey="Fitzpatrick, Michael R" sort="Fitzpatrick, Michael R" uniqKey="Fitzpatrick M" first="Michael R." last="Fitzpatrick">Michael R. Fitzpatrick</name>
<name sortKey="Fitzpatrick, Michael R" sort="Fitzpatrick, Michael R" uniqKey="Fitzpatrick M" first="Michael R." last="Fitzpatrick">Michael R. Fitzpatrick</name>
<name sortKey="Gaudiello, Eric C" sort="Gaudiello, Eric C" uniqKey="Gaudiello E" first="Eric C." last="Gaudiello">Eric C. Gaudiello</name>
<name sortKey="Gaudiello, Eric C" sort="Gaudiello, Eric C" uniqKey="Gaudiello E" first="Eric C." last="Gaudiello">Eric C. Gaudiello</name>
<name sortKey="Joshi, Trupti" sort="Joshi, Trupti" uniqKey="Joshi T" first="Trupti" last="Joshi">Trupti Joshi</name>
<name sortKey="Joshi, Trupti" sort="Joshi, Trupti" uniqKey="Joshi T" first="Trupti" last="Joshi">Trupti Joshi</name>
<name sortKey="Joshi, Trupti" sort="Joshi, Trupti" uniqKey="Joshi T" first="Trupti" last="Joshi">Trupti Joshi</name>
<name sortKey="Liu, Yang" sort="Liu, Yang" uniqKey="Liu Y" first="Yang" last="Liu">Yang Liu</name>
<name sortKey="Liu, Yang" sort="Liu, Yang" uniqKey="Liu Y" first="Yang" last="Liu">Yang Liu</name>
<name sortKey="Nguyen, Henry T" sort="Nguyen, Henry T" uniqKey="Nguyen H" first="Henry T." last="Nguyen">Henry T. Nguyen</name>
<name sortKey="Nguyen, Henry T" sort="Nguyen, Henry T" uniqKey="Nguyen H" first="Henry T." last="Nguyen">Henry T. Nguyen</name>
<name sortKey="Nguyen, Henry T" sort="Nguyen, Henry T" uniqKey="Nguyen H" first="Henry T." last="Nguyen">Henry T. Nguyen</name>
<name sortKey="Stacey, Gary" sort="Stacey, Gary" uniqKey="Stacey G" first="Gary" last="Stacey">Gary Stacey</name>
<name sortKey="Stacey, Gary" sort="Stacey, Gary" uniqKey="Stacey G" first="Gary" last="Stacey">Gary Stacey</name>
<name sortKey="Stacey, Gary" sort="Stacey, Gary" uniqKey="Stacey G" first="Gary" last="Stacey">Gary Stacey</name>
<name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name>
<name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name>
<name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name>
<name sortKey="Xu, Dong" sort="Xu, Dong" uniqKey="Xu D" first="Dong" last="Xu">Dong Xu</name>
<name sortKey="Zhang, Hongxin" sort="Zhang, Hongxin" uniqKey="Zhang H" first="Hongxin" last="Zhang">Hongxin Zhang</name>
<name sortKey="Zhang, Hongxin" sort="Zhang, Hongxin" uniqKey="Zhang H" first="Hongxin" last="Zhang">Hongxin Zhang</name>
</country>
</tree>
</affiliations>
</record>

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