Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource
Identifieur interne : 000583 ( Pmc/Curation ); précédent : 000582; suivant : 000584Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource
Auteurs : Shulei Sun ; Jing Chen ; Weizhong Li ; Ilkay Altintas ; Abel Lin ; Steve Peltier ; Karen Stocks ; Eric E. Allen ; Mark Ellisman ; Jeffrey Grethe ; John WooleySource :
- Nucleic Acids Research [ 0305-1048 ] ; 2010.
Abstract
The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA,
Url:
DOI: 10.1093/nar/gkq1102
PubMed: 21045053
PubMed Central: 3013694
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<author><name sortKey="Chen, Jing" sort="Chen, Jing" uniqKey="Chen J" first="Jing" last="Chen">Jing Chen</name>
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<author><name sortKey="Stocks, Karen" sort="Stocks, Karen" uniqKey="Stocks K" first="Karen" last="Stocks">Karen Stocks</name>
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<author><name sortKey="Allen, Eric E" sort="Allen, Eric E" uniqKey="Allen E" first="Eric E." last="Allen">Eric E. Allen</name>
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<author><name sortKey="Ellisman, Mark" sort="Ellisman, Mark" uniqKey="Ellisman M" first="Mark" last="Ellisman">Mark Ellisman</name>
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource</title>
<author><name sortKey="Sun, Shulei" sort="Sun, Shulei" uniqKey="Sun S" first="Shulei" last="Sun">Shulei Sun</name>
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<author><name sortKey="Chen, Jing" sort="Chen, Jing" uniqKey="Chen J" first="Jing" last="Chen">Jing Chen</name>
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<author><name sortKey="Li, Weizhong" sort="Li, Weizhong" uniqKey="Li W" first="Weizhong" last="Li">Weizhong Li</name>
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<author><name sortKey="Altintas, Ilkay" sort="Altintas, Ilkay" uniqKey="Altintas I" first="Ilkay" last="Altintas">Ilkay Altintas</name>
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<author><name sortKey="Lin, Abel" sort="Lin, Abel" uniqKey="Lin A" first="Abel" last="Lin">Abel Lin</name>
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<author><name sortKey="Peltier, Steve" sort="Peltier, Steve" uniqKey="Peltier S" first="Steve" last="Peltier">Steve Peltier</name>
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<author><name sortKey="Stocks, Karen" sort="Stocks, Karen" uniqKey="Stocks K" first="Karen" last="Stocks">Karen Stocks</name>
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<author><name sortKey="Allen, Eric E" sort="Allen, Eric E" uniqKey="Allen E" first="Eric E." last="Allen">Eric E. Allen</name>
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<author><name sortKey="Ellisman, Mark" sort="Ellisman, Mark" uniqKey="Ellisman M" first="Mark" last="Ellisman">Mark Ellisman</name>
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<author><name sortKey="Grethe, Jeffrey" sort="Grethe, Jeffrey" uniqKey="Grethe J" first="Jeffrey" last="Grethe">Jeffrey Grethe</name>
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<author><name sortKey="Wooley, John" sort="Wooley, John" uniqKey="Wooley J" first="John" last="Wooley">John Wooley</name>
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<series><title level="j">Nucleic Acids Research</title>
<idno type="ISSN">0305-1048</idno>
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<front><div type="abstract" xml:lang="en"><p>The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, <ext-link ext-link-type="uri" xlink:href="http://camera.calit2.net/">http://camera.calit2.net/</ext-link>
) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets, and supports pre-registration of samples for sequencing. CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data.</p>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">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><journal-title>Nucleic Acids Research</journal-title>
</journal-title-group>
<issn pub-type="ppub">0305-1048</issn>
<issn pub-type="epub">1362-4962</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">21045053</article-id>
<article-id pub-id-type="pmc">3013694</article-id>
<article-id pub-id-type="doi">10.1093/nar/gkq1102</article-id>
<article-id pub-id-type="publisher-id">gkq1102</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Articles</subject>
</subj-group>
</article-categories>
<title-group><article-title>Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Sun</surname>
<given-names>Shulei</given-names>
</name>
<xref ref-type="corresp" rid="COR1">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chen</surname>
<given-names>Jing</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Li</surname>
<given-names>Weizhong</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Altintas</surname>
<given-names>Ilkay</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Lin</surname>
<given-names>Abel</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Peltier</surname>
<given-names>Steve</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Stocks</surname>
<given-names>Karen</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Allen</surname>
<given-names>Eric E.</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Ellisman</surname>
<given-names>Mark</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Grethe</surname>
<given-names>Jeffrey</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Wooley</surname>
<given-names>John</given-names>
</name>
</contrib>
</contrib-group>
<aff>The CAMERA Project, Center for Research on Biological Systems and California Institute of Telecommunication and Information Technology, University of California San Diego, 9500 Gilman Drive, Mail Code 0446 92093-5004, USA</aff>
<author-notes><corresp id="COR1">*To whom correspondence should be addressed. Tel: <phone>858-822-0929</phone>
; Fax: <fax>858-822-0828</fax>
; Email: <email>s2sun@ucsd.edu</email>
; <email>shuleisun@gmail.com</email>
</corresp>
</author-notes>
<pmc-comment>For NAR both ppub and collection dates generated for PMC processing 1/27/05 beck</pmc-comment>
<pub-date pub-type="collection"><month>1</month>
<year>2011</year>
</pub-date>
<pub-date pub-type="ppub"><month>1</month>
<year>2011</year>
</pub-date>
<pub-date pub-type="epub"><day>2</day>
<month>11</month>
<year>2010</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>2</day>
<month>11</month>
<year>2010</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
. </pmc-comment>
<volume>39</volume>
<issue>Database issue</issue>
<issue-title>Database issue</issue-title>
<fpage>D546</fpage>
<lpage>D551</lpage>
<history><date date-type="received"><day>27</day>
<month>8</month>
<year>2010</year>
</date>
<date date-type="rev-recd"><day>15</day>
<month>10</month>
<year>2010</year>
</date>
<date date-type="accepted"><day>18</day>
<month>10</month>
<year>2010</year>
</date>
</history>
<permissions><copyright-statement>© The Author(s) 2010. Published by Oxford University Press.</copyright-statement>
<copyright-year>2010</copyright-year>
<license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.5"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.5">http://creativecommons.org/licenses/by-nc/2.5</ext-link>
), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
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<abstract><p>The Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis (CAMERA, <ext-link ext-link-type="uri" xlink:href="http://camera.calit2.net/">http://camera.calit2.net/</ext-link>
) is a database and associated computational infrastructure that provides a single system for depositing, locating, analyzing, visualizing and sharing data about microbial biology through an advanced web-based analysis portal. CAMERA collects and links metadata relevant to environmental metagenome data sets with annotation in a semantically-aware environment allowing users to write expressive semantic queries against the database. To meet the needs of the research community, users are able to query metadata categories such as habitat, sample type, time, location and other environmental physicochemical parameters. CAMERA is compliant with the standards promulgated by the Genomic Standards Consortium (GSC), and sustains a role within the GSC in extending standards for content and format of the metagenomic data and metadata and its submission to the CAMERA repository. To ensure wide, ready access to data and annotation, CAMERA also provides data submission tools to allow researchers to share and forward data to other metagenomics sites and community data archives such as GenBank. It has multiple interfaces for easy submission of large or complex data sets, and supports pre-registration of samples for sequencing. CAMERA integrates a growing list of tools and viewers for querying, analyzing, annotating and comparing metagenome and genome data.</p>
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