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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence</title><author><name sortKey="Sahoo, Satya S" sort="Sahoo, Satya S" uniqKey="Sahoo S" first="Satya S." last="Sahoo">Satya S. Sahoo</name><affiliation><nlm:aff id="A1">Kno.e.sis Center, Wright State University, Dayton, OH</nlm:aff></affiliation><affiliation><nlm:aff id="A2">LHNCBC, National Library of Medicine, Bethesda, MD</nlm:aff></affiliation></author><author><name sortKey="Bodenreider, Olivier" sort="Bodenreider, Olivier" uniqKey="Bodenreider O" first="Olivier" last="Bodenreider">Olivier Bodenreider</name><affiliation><nlm:aff id="A2">LHNCBC, National Library of Medicine, Bethesda, MD</nlm:aff></affiliation></author><author><name sortKey="Rutter, Joni L" sort="Rutter, Joni L" uniqKey="Rutter J" first="Joni L." last="Rutter">Joni L. Rutter</name><affiliation><nlm:aff id="A3">DBNBR, National Institute on Drug Abuse, Bethesda, MD</nlm:aff></affiliation></author><author><name sortKey="Skinner, Karen J" sort="Skinner, Karen J" uniqKey="Skinner K" first="Karen J." last="Skinner">Karen J. Skinner</name><affiliation><nlm:aff id="A3">DBNBR, National Institute on Drug Abuse, Bethesda, MD</nlm:aff></affiliation></author><author><name sortKey="Sheth, Amit P" sort="Sheth, Amit P" uniqKey="Sheth A" first="Amit P." last="Sheth">Amit P. Sheth</name><affiliation><nlm:aff id="A1">Kno.e.sis Center, Wright State University, Dayton, OH</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">18395495</idno><idno type="pmc">2766186</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766186</idno><idno type="RBID">PMC:2766186</idno><idno type="doi">10.1016/j.jbi.2008.02.006</idno><date when="2008">2008</date><idno type="wicri:Area/Pmc/Corpus">000284</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence</title><author><name sortKey="Sahoo, Satya S" sort="Sahoo, Satya S" uniqKey="Sahoo S" first="Satya S." last="Sahoo">Satya S. Sahoo</name><affiliation><nlm:aff id="A1">Kno.e.sis Center, Wright State University, Dayton, OH</nlm:aff></affiliation><affiliation><nlm:aff id="A2">LHNCBC, National Library of Medicine, Bethesda, MD</nlm:aff></affiliation></author><author><name sortKey="Bodenreider, Olivier" sort="Bodenreider, Olivier" uniqKey="Bodenreider O" first="Olivier" last="Bodenreider">Olivier Bodenreider</name><affiliation><nlm:aff id="A2">LHNCBC, National Library of Medicine, Bethesda, MD</nlm:aff></affiliation></author><author><name sortKey="Rutter, Joni L" sort="Rutter, Joni L" uniqKey="Rutter J" first="Joni L." last="Rutter">Joni L. Rutter</name><affiliation><nlm:aff id="A3">DBNBR, National Institute on Drug Abuse, Bethesda, MD</nlm:aff></affiliation></author><author><name sortKey="Skinner, Karen J" sort="Skinner, Karen J" uniqKey="Skinner K" first="Karen J." last="Skinner">Karen J. Skinner</name><affiliation><nlm:aff id="A3">DBNBR, National Institute on Drug Abuse, Bethesda, MD</nlm:aff></affiliation></author><author><name sortKey="Sheth, Amit P" sort="Sheth, Amit P" uniqKey="Sheth A" first="Amit P." last="Sheth">Amit P. Sheth</name><affiliation><nlm:aff id="A1">Kno.e.sis Center, Wright State University, Dayton, OH</nlm:aff></affiliation></author></analytic><series><title level="j">Journal of biomedical informatics</title><idno type="ISSN">1532-0464</idno><idno type="eISSN">1532-0480</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec id="S1"><title>Objectives</title><p id="P1">This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base.</p></sec><sec sec-type="methods" id="S2"><title>Methods</title><p id="P2">We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries.</p></sec><sec id="S3"><title>Results</title><p id="P3">Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins.</p></sec><sec id="S4"><title>Conclusion</title><p id="P4">Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces.</p></sec><sec id="S5"><title>Resource page</title><p id="P5"><ext-link ext-link-type="uri" xlink:href="http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/">http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/</ext-link></p></sec></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">100970413</journal-id><journal-id journal-id-type="pubmed-jr-id">22289</journal-id><journal-id journal-id-type="nlm-ta">J Biomed Inform</journal-id><journal-title>Journal of biomedical informatics</journal-title><issn pub-type="ppub">1532-0464</issn><issn pub-type="epub">1532-0480</issn></journal-meta><article-meta><article-id pub-id-type="pmid">18395495</article-id><article-id pub-id-type="pmc">2766186</article-id><article-id pub-id-type="manuscript">NIHMS74431</article-id><article-id pub-id-type="doi">10.1016/j.jbi.2008.02.006</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Sahoo</surname><given-names>Satya S.</given-names></name><xref ref-type="aff" rid="A1">1</xref><xref ref-type="aff" rid="A2">2</xref></contrib><contrib contrib-type="author"><name><surname>Bodenreider</surname><given-names>Olivier</given-names></name><xref ref-type="aff" rid="A2">2</xref><xref ref-type="corresp" rid="cor1">$</xref></contrib><contrib contrib-type="author"><name><surname>Rutter</surname><given-names>Joni L.</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Skinner</surname><given-names>Karen J.</given-names></name><xref ref-type="aff" rid="A3">3</xref></contrib><contrib contrib-type="author"><name><surname>Sheth</surname><given-names>Amit P.</given-names></name><xref ref-type="aff" rid="A1">1</xref></contrib></contrib-group><aff id="A1"><label>1</label>Kno.e.sis Center, Wright State University, Dayton, OH</aff><aff id="A2"><label>2</label>LHNCBC, National Library of Medicine, Bethesda, MD</aff><aff id="A3"><label>3</label>DBNBR, National Institute on Drug Abuse, Bethesda, MD</aff><author-notes><corresp id="cor1"><label>$</label>Corresponding author: Dr. Olivier Bodenreider, National Library of Medicine, 8600 Rockville Pike - MS 3841 (Bldg 38A, Rm B1N28U), Bethesda, MD 20894 - USA, phone: 301 435-3246 - fax: 301 480-3035, <email>olivier@nlm.nih.gov</email></corresp></author-notes><pub-date pub-type="nihms-submitted"><day>17</day><month>10</month><year>2008</year></pub-date><pub-date pub-type="epub"><day>29</day><month>2</month><year>2008</year></pub-date><pub-date pub-type="ppub"><month>10</month><year>2008</year></pub-date><pub-date pub-type="pmc-release"><day>23</day><month>10</month><year>2009</year></pub-date><volume>41</volume><issue>5</issue><fpage>752</fpage><lpage>765</lpage><permissions><copyright-statement>© 2008 Elsevier Inc. All rights reserved.</copyright-statement><copyright-year>2008</copyright-year></permissions><abstract><sec id="S1"><title>Objectives</title><p id="P1">This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base.</p></sec><sec sec-type="methods" id="S2"><title>Methods</title><p id="P2">We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries.</p></sec><sec id="S3"><title>Results</title><p id="P3">Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins.</p></sec><sec id="S4"><title>Conclusion</title><p id="P4">Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces.</p></sec><sec id="S5"><title>Resource page</title><p id="P5"><ext-link ext-link-type="uri" xlink:href="http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/">http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/</ext-link></p></sec></abstract><kwd-group><kwd>Semantic Web</kwd><kwd>Semantic mashup</kwd><kwd>Nicotine dependence</kwd><kwd>Information integration</kwd><kwd>Ontologies</kwd></kwd-group><contract-num rid="PHS2">NIH0010520108</contract-num><contract-sponsor id="PHS2">NIH Intramural Employee : PHS</contract-sponsor></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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