Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees
Identifieur interne : 000517 ( Pmc/Curation ); précédent : 000516; suivant : 000518Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees
Auteurs : Qinghua Wang [États-Unis] ; Cecilia N. Arighi [États-Unis] ; Benjamin L. King [États-Unis] ; Shawn W. Polson [États-Unis] ; James Vincent [États-Unis] ; Chuming Chen [États-Unis] ; Hongzhan Huang [États-Unis] ; Brewster F. Kingham [États-Unis] ; Shallee T. Page [États-Unis] ; Marc Farnum Rendino [États-Unis] ; William Kelley Thomas [États-Unis] ; Daniel W. Udwary [États-Unis] ; Cathy H. Wu [États-Unis]Source :
- Database: The Journal of Biological Databases and Curation [ 1758-0463 ] ; 2012.
Abstract
Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (
Url:
DOI: 10.1093/database/bar064
PubMed: 22434832
PubMed Central: 3308154
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<front><div type="abstract" xml:lang="en"><p>Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (<italic>Leucoraja erinacea</italic>
) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (<ext-link ext-link-type="uri" xlink:href="http://skatebase.org">http://skatebase.org</ext-link>
) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the <italic>L. erinacea</italic>
genome.</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">Database (Oxford)</journal-id>
<journal-id journal-id-type="iso-abbrev">Database (Oxford)</journal-id>
<journal-id journal-id-type="publisher-id">databa</journal-id>
<journal-id journal-id-type="hwp">databa</journal-id>
<journal-title-group><journal-title>Database: The Journal of Biological Databases and Curation</journal-title>
</journal-title-group>
<issn pub-type="epub">1758-0463</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">22434832</article-id>
<article-id pub-id-type="pmc">3308154</article-id>
<article-id pub-id-type="doi">10.1093/database/bar064</article-id>
<article-id pub-id-type="publisher-id">bar064</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Original Articles</subject>
</subj-group>
</article-categories>
<title-group><article-title>Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Wang</surname>
<given-names>Qinghua</given-names>
</name>
<xref ref-type="aff" rid="bar064-AFF1"><sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="bar064-FN1"><sup>†</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Arighi</surname>
<given-names>Cecilia N.</given-names>
</name>
<xref ref-type="aff" rid="bar064-AFF1"><sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="bar064-FN1"><sup>†</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>King</surname>
<given-names>Benjamin L.</given-names>
</name>
<xref ref-type="aff" rid="bar064-AFF1"><sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="bar064-FN1"><sup>†</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Polson</surname>
<given-names>Shawn W.</given-names>
</name>
<xref ref-type="aff" rid="bar064-AFF1"><sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="bar064-FN1"><sup>†</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Vincent</surname>
<given-names>James</given-names>
</name>
<xref ref-type="aff" rid="bar064-AFF1"><sup>3</sup>
</xref>
<xref ref-type="author-notes" rid="bar064-FN1"><sup>†</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Chen</surname>
<given-names>Chuming</given-names>
</name>
<xref ref-type="aff" rid="bar064-AFF1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Huang</surname>
<given-names>Hongzhan</given-names>
</name>
<xref ref-type="aff" rid="bar064-AFF1"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Kingham</surname>
<given-names>Brewster F.</given-names>
</name>
<xref ref-type="aff" rid="bar064-AFF1"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Page</surname>
<given-names>Shallee T.</given-names>
</name>
<xref ref-type="aff" rid="bar064-AFF1"><sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Farnum Rendino</surname>
<given-names>Marc</given-names>
</name>
<xref ref-type="aff" rid="bar064-AFF1"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Thomas</surname>
<given-names>William Kelley</given-names>
</name>
<xref ref-type="aff" rid="bar064-AFF1"><sup>6</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Udwary</surname>
<given-names>Daniel W.</given-names>
</name>
<xref ref-type="aff" rid="bar064-AFF1"><sup>7</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Wu</surname>
<given-names>Cathy H.</given-names>
</name>
<xref ref-type="aff" rid="bar064-AFF1"><sup>1</sup>
</xref>
<xref ref-type="corresp" rid="bar064-COR1">*</xref>
</contrib>
<contrib contrib-type="author"><collab>the North East Bioinformatics Collaborative Curation Team</collab>
<xref ref-type="author-notes" rid="bar064-FN2"><sup>‡</sup>
</xref>
</contrib>
</contrib-group>
<aff id="bar064-AFF1"><sup>1</sup>
Department of Computer and Information Sciences, Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE 19711,<sup>2</sup>
Mount Dessert Island Biological Laboratory, Salisbury Cove, ME 04672,<sup>3</sup>
Vermont Genetics Network, University of Vermont, Burlington, VT 05405,<sup>4</sup>
Sequencing and Genotyping Center, University of Delaware, Newark, DE 19711,<sup>5</sup>
Department of Environmental and Biological Sciences, University of Maine at Machias, Machias, ME 04654,<sup>6</sup>
Department of Molecular Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824 and<sup>7</sup>
Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA</aff>
<author-notes><corresp id="bar064-COR1">*<bold>Corresponding author</bold>
: Tel: <phone>+302 831 8869</phone>
; Fax: <fax>+302 831 4841</fax>
; Email: <email>wuc@udel.edu</email>
</corresp>
<fn id="bar064-FN1"><p><sup>†</sup>
These authors contributed equally to this work.</p>
</fn>
<fn id="bar064-FN2"><p><sup>‡</sup>
The members of the North East Bioinformatics Collaborative (NEBC) Curation Team are provided in the ‘Acknowledgements’ section.</p>
</fn>
</author-notes>
<pub-date pub-type="collection"><year>2012</year>
</pub-date>
<pub-date pub-type="epub"><day>13</day>
<month>2</month>
<year>2012</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>13</day>
<month>2</month>
<year>2012</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
. </pmc-comment>
<volume>2012</volume>
<elocation-id>bar064</elocation-id>
<history><date date-type="received"><day>17</day>
<month>11</month>
<year>2011</year>
</date>
<date date-type="rev-recd"><day>7</day>
<month>12</month>
<year>2011</year>
</date>
<date date-type="accepted"><day>8</day>
<month>12</month>
<year>2011</year>
</date>
</history>
<permissions><copyright-statement>© The Author(s) 2012. Published by Oxford University Press.</copyright-statement>
<copyright-year>2012</copyright-year>
<license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/3.0"><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/3.0">http://creativecommons.org/licenses/by-nc/3.0</ext-link>
), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<abstract><p>Recent advances in high-throughput DNA sequencing technologies have equipped biologists with a powerful new set of tools for advancing research goals. The resulting flood of sequence data has made it critically important to train the next generation of scientists to handle the inherent bioinformatic challenges. The North East Bioinformatics Collaborative (NEBC) is undertaking the genome sequencing and annotation of the little skate (<italic>Leucoraja erinacea</italic>
) to promote advancement of bioinformatics infrastructure in our region, with an emphasis on practical education to create a critical mass of informatically savvy life scientists. In support of the Little Skate Genome Project, the NEBC members have developed several annotation workshops and jamborees to provide training in genome sequencing, annotation and analysis. Acting as a nexus for both curation activities and dissemination of project data, a project web portal, SkateBase (<ext-link ext-link-type="uri" xlink:href="http://skatebase.org">http://skatebase.org</ext-link>
) has been developed. As a case study to illustrate effective coupling of community annotation with workforce development, we report the results of the Mitochondrial Genome Annotation Jamborees organized to annotate the first completely assembled element of the Little Skate Genome Project, as a culminating experience for participants from our three prior annotation workshops. We are applying the physical/virtual infrastructure and lessons learned from these activities to enhance and streamline the genome annotation workflow, as we look toward our continuing efforts for larger-scale functional and structural community annotation of the <italic>L. erinacea</italic>
genome.</p>
</abstract>
<counts><page-count count="11"></page-count>
</counts>
</article-meta>
</front>
</pmc>
</record>
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