THE CELL CENTERED DATABASE PROJECT: AN UPDATE ON BUILDING COMMUNITY RESOURCES FOR MANAGING AND SHARING 3D IMAGING DATA
Identifieur interne : 000301 ( Pmc/Corpus ); précédent : 000300; suivant : 000302THE CELL CENTERED DATABASE PROJECT: AN UPDATE ON BUILDING COMMUNITY RESOURCES FOR MANAGING AND SHARING 3D IMAGING DATA
Auteurs : Maryann E. Martone ; Joshua Tran ; Willy W. Wong ; Joy Sargis ; Lisa Fong ; Stephen Larson ; Stephan P. Lamont ; Amarnath Gupta ; Mark H. EllismanSource :
- Journal of structural biology [ 1047-8477 ] ; 2007.
Abstract
Databases have become integral parts of data management, dissemination and mining in biology. At the Second Annual Conference on Electron Tomography, held in Amsterdam in 2001, we proposed that electron tomography data should be shared in a manner analogous to structural data at the protein and sequence scales. At that time, we outlined our progress in creating a database to bring together cell level imaging data across scales, The Cell Centered Database (CCDB). The CCDB was formally launched in 2002 as an on-line repository of high-resolution 3D light and electron microscopic reconstructions of cells and subcellular structures. It contains 2D, 3D and 4D structural and protein distribution information from confocal, multiphoton and electron microscopy, including correlated light and electron microscopy. Many of the data sets are derived from electron tomography of cells and tissues. In the five years since its debut, we have moved the CCDB from a prototype to a stable resource and expanded the scope of the project to include data management and knowledge engineering. Here we provide an update on the CCDB and how it is used by the scientific community. We also describe our work in developing additional knowledge tools, e.g., ontologies, for annotation and query of electron microscopic data.
Url:
DOI: 10.1016/j.jsb.2007.10.003
PubMed: 18054501
PubMed Central: 2367257
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PMC:2367257Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">THE CELL CENTERED DATABASE PROJECT: AN UPDATE ON BUILDING COMMUNITY RESOURCES FOR MANAGING AND SHARING 3D IMAGING DATA</title>
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<author><name sortKey="Gupta, Amarnath" sort="Gupta, Amarnath" uniqKey="Gupta A" first="Amarnath" last="Gupta">Amarnath Gupta</name>
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<series><title level="j">Journal of structural biology</title>
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<front><div type="abstract" xml:lang="en"><p id="P1">Databases have become integral parts of data management, dissemination and mining in biology. At the Second Annual Conference on Electron Tomography, held in Amsterdam in 2001, we proposed that electron tomography data should be shared in a manner analogous to structural data at the protein and sequence scales. At that time, we outlined our progress in creating a database to bring together cell level imaging data across scales, The Cell Centered Database (CCDB). The CCDB was formally launched in 2002 as an on-line repository of high-resolution 3D light and electron microscopic reconstructions of cells and subcellular structures. It contains 2D, 3D and 4D structural and protein distribution information from confocal, multiphoton and electron microscopy, including correlated light and electron microscopy. Many of the data sets are derived from electron tomography of cells and tissues. In the five years since its debut, we have moved the CCDB from a prototype to a stable resource and expanded the scope of the project to include data management and knowledge engineering. Here we provide an update on the CCDB and how it is used by the scientific community. We also describe our work in developing additional knowledge tools, e.g., ontologies, for annotation and query of electron microscopic data.</p>
</div>
</front>
</TEI>
<pmc article-type="research-article" xml:lang="EN"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<pmc-dir>properties manuscript</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-journal-id">9011206</journal-id>
<journal-id journal-id-type="pubmed-jr-id">1746</journal-id>
<journal-id journal-id-type="nlm-ta">J Struct Biol</journal-id>
<journal-title>Journal of structural biology</journal-title>
<issn pub-type="ppub">1047-8477</issn>
<issn pub-type="epub">1095-8657</issn>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">18054501</article-id>
<article-id pub-id-type="pmc">2367257</article-id>
<article-id pub-id-type="doi">10.1016/j.jsb.2007.10.003</article-id>
<article-id pub-id-type="manuscript">NIHMS44054</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>THE CELL CENTERED DATABASE PROJECT: AN UPDATE ON BUILDING COMMUNITY RESOURCES FOR MANAGING AND SHARING 3D IMAGING DATA</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Martone</surname>
<given-names>Maryann E.</given-names>
</name>
<xref rid="A1" ref-type="aff">1</xref>
<xref rid="A2" ref-type="aff">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tran</surname>
<given-names>Joshua</given-names>
</name>
<xref rid="A1" ref-type="aff">1</xref>
<xref rid="A2" ref-type="aff">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wong</surname>
<given-names>Willy W.</given-names>
</name>
<xref rid="A1" ref-type="aff">1</xref>
<xref rid="A2" ref-type="aff">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sargis</surname>
<given-names>Joy</given-names>
</name>
<xref rid="A1" ref-type="aff">1</xref>
<xref rid="A2" ref-type="aff">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Fong</surname>
<given-names>Lisa</given-names>
</name>
<xref rid="A1" ref-type="aff">1</xref>
<xref rid="A2" ref-type="aff">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Larson</surname>
<given-names>Stephen</given-names>
</name>
<xref rid="A1" ref-type="aff">1</xref>
<xref rid="A2" ref-type="aff">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lamont</surname>
<given-names>Stephan P.</given-names>
</name>
<xref rid="A1" ref-type="aff">1</xref>
<xref rid="A2" ref-type="aff">2</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Gupta</surname>
<given-names>Amarnath</given-names>
</name>
<xref rid="A2" ref-type="aff">2</xref>
<xref rid="A3" ref-type="aff">3</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ellisman</surname>
<given-names>Mark H.</given-names>
</name>
<xref rid="A1" ref-type="aff">1</xref>
<xref rid="A2" ref-type="aff">2</xref>
</contrib>
</contrib-group>
<aff id="A1"><label>1</label>
Dept of Neurosciences University of California, San Diego, San Diego CA 92093-0608</aff>
<aff id="A2"><label>2</label>
Center for Research in Biological Systems, University of California, San Diego 92093-0446</aff>
<aff id="A3"><label>3</label>
San Diego Supercomputer Center, University of California, San Diego 92093-0515</aff>
<author-notes><corresp id="FN1">Corresponding Author: Maryann E. Martone, Ph. D., Dept of Neurosciences and Center for Research in Biological Systems, University of California, San Diego San Diego, CA 92093-0446, Tel: 858 822 0745, Fax: 858 822 3610, e-mail: <email>mmartone@ucsd.edu</email>
</corresp>
</author-notes>
<pub-date pub-type="nihms-submitted"><day>28</day>
<month>3</month>
<year>2008</year>
</pub-date>
<pub-date pub-type="epub"><day>16</day>
<month>10</month>
<year>2007</year>
</pub-date>
<pub-date pub-type="ppub"><month>3</month>
<year>2008</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>1</day>
<month>3</month>
<year>2009</year>
</pub-date>
<volume>161</volume>
<issue>3</issue>
<fpage>220</fpage>
<lpage>231</lpage>
<abstract><p id="P1">Databases have become integral parts of data management, dissemination and mining in biology. At the Second Annual Conference on Electron Tomography, held in Amsterdam in 2001, we proposed that electron tomography data should be shared in a manner analogous to structural data at the protein and sequence scales. At that time, we outlined our progress in creating a database to bring together cell level imaging data across scales, The Cell Centered Database (CCDB). The CCDB was formally launched in 2002 as an on-line repository of high-resolution 3D light and electron microscopic reconstructions of cells and subcellular structures. It contains 2D, 3D and 4D structural and protein distribution information from confocal, multiphoton and electron microscopy, including correlated light and electron microscopy. Many of the data sets are derived from electron tomography of cells and tissues. In the five years since its debut, we have moved the CCDB from a prototype to a stable resource and expanded the scope of the project to include data management and knowledge engineering. Here we provide an update on the CCDB and how it is used by the scientific community. We also describe our work in developing additional knowledge tools, e.g., ontologies, for annotation and query of electron microscopic data.</p>
</abstract>
<kwd-group><kwd>electron tomography</kwd>
<kwd>bioinformatics</kwd>
<kwd>ontology</kwd>
<kwd>3D reconstruction</kwd>
</kwd-group>
<contract-num rid="NS1">R01 NS058296-01</contract-num>
<contract-num rid="DA1">R01 DA016602-10</contract-num>
<contract-sponsor id="NS1">National Institute of Neurological Disorders and Stroke : NINDS</contract-sponsor>
<contract-sponsor id="DA1">National Institute on Drug Abuse : NIDA</contract-sponsor>
</article-meta>
</front>
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