Text-mining assisted regulatory annotation
Identifieur interne : 000239 ( Pmc/Curation ); précédent : 000238; suivant : 000240Text-mining assisted regulatory annotation
Auteurs : Stein Aerts [Belgique] ; Maximilian Haeussler [France] ; Steven Van Vooren [Belgique] ; Obi L. Griffith [Canada] ; Paco Hulpiau [Belgique] ; Steven Jm Jones [Canada] ; Stephen B. Montgomery [Royaume-Uni] ; Casey M. Bergman [Royaume-Uni]Source :
- Genome Biology [ 1465-6906 ] ; 2008.
Abstract
Text-mining technologies can be integrated with genome annotation systems, increasing the availability of annotated
Url:
DOI: 10.1186/gb-2008-9-2-r31
PubMed: 18271954
PubMed Central: 2374703
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Griffith</name><affiliation wicri:level="1"><nlm:aff id="I5">Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, V5Z 4E6</wicri:regionArea></affiliation></author><author><name sortKey="Hulpiau, Paco" sort="Hulpiau, Paco" uniqKey="Hulpiau P" first="Paco" last="Hulpiau">Paco Hulpiau</name><affiliation wicri:level="1"><nlm:aff id="I6">VIB Department for Molecular Biomedical Research, Ghent University, Ghent, 9052, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>VIB Department for Molecular Biomedical Research, Ghent University, Ghent, 9052</wicri:regionArea></affiliation></author><author><name sortKey="Jones, Steven Jm" sort="Jones, Steven Jm" uniqKey="Jones S" first="Steven Jm" last="Jones">Steven Jm Jones</name><affiliation wicri:level="1"><nlm:aff id="I5">Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, V5Z 4E6</wicri:regionArea></affiliation></author><author><name sortKey="Montgomery, Stephen B" sort="Montgomery, Stephen B" uniqKey="Montgomery S" first="Stephen B" last="Montgomery">Stephen B. Montgomery</name><affiliation wicri:level="1"><nlm:aff id="I7">Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton, CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Bergman, Casey M" sort="Bergman, Casey M" uniqKey="Bergman C" first="Casey M" last="Bergman">Casey M. Bergman</name><affiliation wicri:level="1"><nlm:aff id="I8">Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18271954</idno><idno type="pmc">2374703</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2374703</idno><idno type="RBID">PMC:2374703</idno><idno type="doi">10.1186/gb-2008-9-2-r31</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">000239</idno><idno type="wicri:Area/Pmc/Curation">000239</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Text-mining assisted regulatory annotation</title><author><name sortKey="Aerts, Stein" sort="Aerts, Stein" uniqKey="Aerts S" first="Stein" last="Aerts">Stein Aerts</name><affiliation wicri:level="1"><nlm:aff id="I1">Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, B-3000, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, B-3000</wicri:regionArea></affiliation><affiliation wicri:level="1"><nlm:aff id="I2">Department of Human Genetics, Katholieke Universiteit Leuven School of Medicine, Herestraat, Leuven, B-3000, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Human Genetics, Katholieke Universiteit Leuven School of Medicine, Herestraat, Leuven, B-3000</wicri:regionArea></affiliation></author><author><name sortKey="Haeussler, Maximilian" sort="Haeussler, Maximilian" uniqKey="Haeussler M" first="Maximilian" last="Haeussler">Maximilian Haeussler</name><affiliation wicri:level="1"><nlm:aff id="I3">Institut de Neurosciences A Fessard, Centre National de la Rechere Scientifique, Gif-sur-Yvette, 91 198, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Institut de Neurosciences A Fessard, Centre National de la Rechere Scientifique, Gif-sur-Yvette, 91 198</wicri:regionArea></affiliation></author><author><name sortKey="Van Vooren, Steven" sort="Van Vooren, Steven" uniqKey="Van Vooren S" first="Steven" last="Van Vooren">Steven Van Vooren</name><affiliation wicri:level="1"><nlm:aff id="I4">Department of Electrical Engineering, Katholieke Universiteit Leuven, Heverlee, B-3001, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Electrical Engineering, Katholieke Universiteit Leuven, Heverlee, B-3001</wicri:regionArea></affiliation></author><author><name sortKey="Griffith, Obi L" sort="Griffith, Obi L" uniqKey="Griffith O" first="Obi L" last="Griffith">Obi L. Griffith</name><affiliation wicri:level="1"><nlm:aff id="I5">Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, V5Z 4E6</wicri:regionArea></affiliation></author><author><name sortKey="Hulpiau, Paco" sort="Hulpiau, Paco" uniqKey="Hulpiau P" first="Paco" last="Hulpiau">Paco Hulpiau</name><affiliation wicri:level="1"><nlm:aff id="I6">VIB Department for Molecular Biomedical Research, Ghent University, Ghent, 9052, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>VIB Department for Molecular Biomedical Research, Ghent University, Ghent, 9052</wicri:regionArea></affiliation></author><author><name sortKey="Jones, Steven Jm" sort="Jones, Steven Jm" uniqKey="Jones S" first="Steven Jm" last="Jones">Steven Jm Jones</name><affiliation wicri:level="1"><nlm:aff id="I5">Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, V5Z 4E6, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, V5Z 4E6</wicri:regionArea></affiliation></author><author><name sortKey="Montgomery, Stephen B" sort="Montgomery, Stephen B" uniqKey="Montgomery S" first="Stephen B" last="Montgomery">Stephen B. Montgomery</name><affiliation wicri:level="1"><nlm:aff id="I7">Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Wellcome Trust Sanger Institute, Hinxton, CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Bergman, Casey M" sort="Bergman, Casey M" uniqKey="Bergman C" first="Casey M" last="Bergman">Casey M. Bergman</name><affiliation wicri:level="1"><nlm:aff id="I8">Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT</wicri:regionArea></affiliation></author></analytic><series><title level="j">Genome Biology</title><idno type="ISSN">1465-6906</idno><idno type="eISSN">1465-6914</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Text-mining technologies can be integrated with genome annotation systems, increasing the availability of annotated <italic>cis</italic>-regulatory data.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol</journal-id><journal-title>Genome Biology</journal-title><issn pub-type="ppub">1465-6906</issn><issn pub-type="epub">1465-6914</issn><publisher><publisher-name>BioMed Central</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">18271954</article-id><article-id pub-id-type="pmc">2374703</article-id><article-id pub-id-type="publisher-id">gb-2008-9-2-r31</article-id><article-id pub-id-type="doi">10.1186/gb-2008-9-2-r31</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research</subject></subj-group></article-categories><title-group><article-title>Text-mining assisted regulatory annotation</article-title></title-group><contrib-group><contrib id="A1" corresp="yes" contrib-type="author"><name><surname>Aerts</surname><given-names>Stein</given-names></name><xref ref-type="aff" rid="I1">1</xref><xref ref-type="aff" rid="I2">2</xref><email>stein.aerts@med.kuleuven.be</email></contrib><contrib id="A2" contrib-type="author"><name><surname>Haeussler</surname><given-names>Maximilian</given-names></name><xref ref-type="aff" rid="I3">3</xref><email>maximilianh@gmail.com</email></contrib><contrib id="A3" contrib-type="author"><name><surname>van Vooren</surname><given-names>Steven</given-names></name><xref ref-type="aff" rid="I4">4</xref><email>Steven.VanVooren@esat.kuleuven.ac.be</email></contrib><contrib id="A4" contrib-type="author"><name><surname>Griffith</surname><given-names>Obi L</given-names></name><xref ref-type="aff" rid="I5">5</xref><email>obig@bcgsc.ca</email></contrib><contrib id="A5" contrib-type="author"><name><surname>Hulpiau</surname><given-names>Paco</given-names></name><xref ref-type="aff" rid="I6">6</xref><email>paco.hulpiau@dmbr.ugent.be</email></contrib><contrib id="A6" contrib-type="author"><name><surname>Jones</surname><given-names>Steven JM</given-names></name><xref ref-type="aff" rid="I5">5</xref><email>sjones@bcgsc.ca</email></contrib><contrib id="A7" contrib-type="author"><name><surname>Montgomery</surname><given-names>Stephen B</given-names></name><xref ref-type="aff" rid="I7">7</xref><email>sm8@sanger.ac.uk</email></contrib><contrib id="A8" corresp="yes" contrib-type="author"><name><surname>Bergman</surname><given-names>Casey M</given-names></name><xref ref-type="aff" rid="I8">8</xref><email>casey.bergman@manchester.ac.uk</email></contrib><contrib id="A9" contrib-type="author"><collab>The Open Regulatory Annotation Consortium</collab><email>oreganno@noaddress.com</email></contrib></contrib-group><aff id="I1"><label>1</label>Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, VIB, Leuven, B-3000, Belgium</aff><aff id="I2"><label>2</label>Department of Human Genetics, Katholieke Universiteit Leuven School of Medicine, Herestraat, Leuven, B-3000, Belgium</aff><aff id="I3"><label>3</label>Institut de Neurosciences A Fessard, Centre National de la Rechere Scientifique, Gif-sur-Yvette, 91 198, France</aff><aff id="I4"><label>4</label>Department of Electrical Engineering, Katholieke Universiteit Leuven, Heverlee, B-3001, Belgium</aff><aff id="I5"><label>5</label>Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, V5Z 4E6, Canada</aff><aff id="I6"><label>6</label>VIB Department for Molecular Biomedical Research, Ghent University, Ghent, 9052, Belgium</aff><aff id="I7"><label>7</label>Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK</aff><aff id="I8"><label>8</label>Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK</aff><pub-date pub-type="ppub"><year>2008</year></pub-date><pub-date pub-type="epub"><day>13</day><month>2</month><year>2008</year></pub-date><volume>9</volume><issue>2</issue><fpage>R31</fpage><lpage>R31</lpage><ext-link ext-link-type="uri" xlink:href="http://genomebiology.com/2008/9/2/R31"></ext-link><history><date date-type="received"><day>2</day><month>10</month><year>2007</year></date><date date-type="rev-recd"><day>21</day><month>12</month><year>2007</year></date><date date-type="accepted"><day>13</day><month>2</month><year>2008</year></date></history><permissions><copyright-statement>Copyright © 2008 Aerts et al.; licensee BioMed Central Ltd.</copyright-statement><copyright-year>2008</copyright-year><copyright-holder>Aerts et al.; licensee BioMed Central Ltd.</copyright-holder><license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><p>This is an open access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0"></ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p><pmc-comment>
Aerts
Stein
stein.aerts@med.kuleuven.be
Text-mining assisted regulatory annotation
2008 Genome Biology 9(2): R31-. (2008) 1465-6906(2008)9:2 urn:ISSN:1465-6906
</license></permissions><abstract abstract-type="short"><p>Text-mining technologies can be integrated with genome annotation systems, increasing the availability of annotated <italic>cis</italic>-regulatory data.</p></abstract><abstract><sec><title>Background</title><p>Decoding transcriptional regulatory networks and the genomic <italic>cis</italic>-regulatory logic implemented in their control nodes is a fundamental challenge in genome biology. High-throughput computational and experimental analyses of regulatory networks and sequences rely heavily on positive control data from prior small-scale experiments, but the vast majority of previously discovered regulatory data remains locked in the biomedical literature.</p></sec><sec><title>Results</title><p>We develop text-mining strategies to identify relevant publications and extract sequence information to assist the regulatory annotation process. Using a vector space model to identify Medline abstracts from papers likely to have high <italic>cis</italic>-regulatory content, we demonstrate that document relevance ranking can assist the curation of transcriptional regulatory networks and estimate that, minimally, 30,000 papers harbor unannotated <italic>cis</italic>-regulatory data. In addition, we show that DNA sequences can be extracted from primary text with high <italic>cis</italic>-regulatory content and mapped to genome sequences as a means of identifying the location, organism and target gene information that is critical to the <italic>cis</italic>-regulatory annotation process.</p></sec><sec><title>Conclusion</title><p>Our results demonstrate that text-mining technologies can be successfully integrated with genome annotation systems, thereby increasing the availability of annotated <italic>cis</italic>-regulatory data needed to catalyze advances in the field of gene regulation.</p></sec></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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