NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources
Identifieur interne : 000051 ( Pmc/Curation ); précédent : 000050; suivant : 000052NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources
Auteurs : Clement Jonquet [États-Unis, France] ; Paea Lependu [États-Unis] ; Sean Falconer [États-Unis] ; Adrien Coulet [États-Unis, France] ; Natalya F. Noy [États-Unis] ; Mark A. Musen [États-Unis] ; Nigam H. Shah [États-Unis]Source :
- Web semantics (Online) [ 1570-8268 ] ; 2011.
Abstract
The volume of publicly available data in biomedicine is constantly increasing. However, these data are stored in different formats and on different platforms. Integrating these data will enable us to facilitate the pace of medical discoveries by providing scientists with a unified view of this diverse information. Under the auspices of the National Center for Biomedical Ontology (NCBO), we have developed the Resource Index—a growing, large-scale ontology-based index of more than twenty heterogeneous biomedical resources. The resources come from a variety of repositories maintained by organizations from around the world. We use a set of over 200 publicly available ontologies contributed by researchers in various domains to annotate the elements in these resources. We use the semantics that the ontologies encode, such as different properties of classes, the class hierarchies, and the mappings between ontologies, in order to improve the search experience for the Resource Index user. Our user interface enables scientists to search the multiple resources quickly and efficiently using domain terms, without even being aware that there is semantics “under the hood.”
Url:
DOI: 10.1016/j.websem.2011.06.005
PubMed: 21918645
PubMed Central: 3170774
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Noy</name><affiliation wicri:level="1"><nlm:aff id="A1">Stanford Center for Biomedical Informatics Research, Stanford University, 251 Campus Drive, Stanford, CA 94305-5479, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Stanford Center for Biomedical Informatics Research, Stanford University, 251 Campus Drive, Stanford, CA 94305-5479</wicri:regionArea></affiliation></author><author><name sortKey="Musen, Mark A" sort="Musen, Mark A" uniqKey="Musen M" first="Mark A." last="Musen">Mark A. Musen</name><affiliation wicri:level="1"><nlm:aff id="A1">Stanford Center for Biomedical Informatics Research, Stanford University, 251 Campus Drive, Stanford, CA 94305-5479, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Stanford Center for Biomedical Informatics Research, Stanford University, 251 Campus Drive, Stanford, CA 94305-5479</wicri:regionArea></affiliation></author><author><name sortKey="Shah, Nigam H" sort="Shah, Nigam H" uniqKey="Shah N" first="Nigam H." last="Shah">Nigam H. Shah</name><affiliation wicri:level="1"><nlm:aff id="A1">Stanford Center for Biomedical Informatics Research, Stanford University, 251 Campus Drive, Stanford, CA 94305-5479, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Stanford Center for Biomedical Informatics Research, Stanford University, 251 Campus Drive, Stanford, CA 94305-5479</wicri:regionArea></affiliation></author></analytic><series><title level="j">Web semantics (Online)</title><idno type="ISSN">1570-8268</idno><idno type="eISSN">1873-7749</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P2">The volume of publicly available data in biomedicine is constantly increasing. However, these data are stored in different formats and on different platforms. Integrating these data will enable us to facilitate the pace of medical discoveries by providing scientists with a unified view of this diverse information. Under the auspices of the National Center for Biomedical Ontology (NCBO), we have developed the Resource Index—a growing, large-scale ontology-based index of more than twenty heterogeneous biomedical resources. The resources come from a variety of repositories maintained by organizations from around the world. We use a set of over 200 publicly available ontologies contributed by researchers in various domains to annotate the elements in these resources. We use the semantics that the ontologies encode, such as different properties of classes, the class hierarchies, and the mappings between ontologies, in order to improve the search experience for the Resource Index user. Our user interface enables scientists to search the multiple resources quickly and efficiently using domain terms, without even being aware that there is semantics “under the hood.”</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">101214428</journal-id><journal-id journal-id-type="pubmed-jr-id">33257</journal-id><journal-id journal-id-type="nlm-ta">Web Semant</journal-id><journal-title-group><journal-title>Web semantics (Online)</journal-title></journal-title-group><issn pub-type="ppub">1570-8268</issn><issn pub-type="epub">1873-7749</issn></journal-meta><article-meta><article-id pub-id-type="pmid">21918645</article-id><article-id pub-id-type="pmc">3170774</article-id><article-id pub-id-type="doi">10.1016/j.websem.2011.06.005</article-id><article-id pub-id-type="manuscript">NIHMS308183</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>NCBO Resource Index: Ontology-Based Search and Mining of Biomedical Resources</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Jonquet</surname><given-names>Clement</given-names></name><xref rid="FN1" ref-type="author-notes">*</xref><xref rid="A1" ref-type="aff">a</xref><xref rid="A2" ref-type="aff">b</xref></contrib><contrib contrib-type="author"><name><surname>LePendu</surname><given-names>Paea</given-names></name><xref rid="A1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Falconer</surname><given-names>Sean</given-names></name><xref rid="A1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Coulet</surname><given-names>Adrien</given-names></name><xref rid="A1" ref-type="aff">a</xref><xref rid="A3" ref-type="aff">c</xref></contrib><contrib contrib-type="author"><name><surname>Noy</surname><given-names>Natalya F.</given-names></name><xref rid="A1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Musen</surname><given-names>Mark A.</given-names></name><xref rid="A1" ref-type="aff">a</xref></contrib><contrib contrib-type="author"><name><surname>Shah</surname><given-names>Nigam H.</given-names></name><xref rid="FN1" ref-type="author-notes">*</xref><xref rid="A1" ref-type="aff">a</xref><xref rid="FN2" ref-type="author-notes">1</xref></contrib></contrib-group><aff id="A1"><label>a</label>Stanford Center for Biomedical Informatics Research, Stanford University, 251 Campus Drive, Stanford, CA 94305-5479, USA</aff><aff id="A2"><label>b</label>Laboratory of Informatics, Robotics, and Microelectronics of Montpellier (LIRMM), University of Montpellier, 161 rue Ada, 34095 Montpellier, Cdx 5, France</aff><aff id="A3"><label>c</label>Lorraine Informatics Research and Applications Laboratory (LORIA) – INRIA Nancy - Grand-Est, Campus Scientifique - BP 239, 54506 Vandoeuvre-lès-Nancy Cedex, France</aff><author-notes><corresp id="FN1"><label>*</label>Corresponding authors: <email>jonquet@lirmm.fr</email> (Clement Jonquet), <email>nigam@stanford.edu</email> (Nigam H. Shah)</corresp><fn id="FN2"><label>1</label><p>Tel: 001 650-725-6236, Fax: 001 650-725-7944</p></fn></author-notes><pub-date pub-type="nihms-submitted"><day>13</day><month>7</month><year>2011</year></pub-date><pub-date pub-type="ppub"><day>1</day><month>9</month><year>2011</year></pub-date><pub-date pub-type="pmc-release"><day>1</day><month>9</month><year>2012</year></pub-date><volume>9</volume><issue>3</issue><fpage>316</fpage><lpage>324</lpage><permissions><copyright-statement>© 2011 Elsevier B.V. All rights reserved.</copyright-statement><copyright-year>2011</copyright-year></permissions><self-uri xlink:href="http://www.sciencedirect.com/science/article/pii/S1570826811000485"></self-uri><abstract><p id="P2">The volume of publicly available data in biomedicine is constantly increasing. However, these data are stored in different formats and on different platforms. Integrating these data will enable us to facilitate the pace of medical discoveries by providing scientists with a unified view of this diverse information. Under the auspices of the National Center for Biomedical Ontology (NCBO), we have developed the Resource Index—a growing, large-scale ontology-based index of more than twenty heterogeneous biomedical resources. The resources come from a variety of repositories maintained by organizations from around the world. We use a set of over 200 publicly available ontologies contributed by researchers in various domains to annotate the elements in these resources. We use the semantics that the ontologies encode, such as different properties of classes, the class hierarchies, and the mappings between ontologies, in order to improve the search experience for the Resource Index user. Our user interface enables scientists to search the multiple resources quickly and efficiently using domain terms, without even being aware that there is semantics “under the hood.”</p></abstract><kwd-group><kwd>semantic Web</kwd><kwd>ontology-based indexing</kwd><kwd>semantic annotation</kwd><kwd>data integration</kwd><kwd>information mining</kwd><kwd>information retrieval</kwd><kwd>biomedical data</kwd><kwd>biomedical ontologies</kwd></kwd-group><funding-group><award-group><funding-source country="United States">National Human Genome Research Institute : NHGRI</funding-source><award-id>U54 HG004028-05 || HG</award-id></award-group><award-group><funding-source country="United States">National Human Genome Research Institute : NHGRI</funding-source><award-id>U54 HG004028-04 || HG</award-id></award-group><award-group><funding-source country="United States">National Human Genome Research Institute : NHGRI</funding-source><award-id>U54 HG004028-03 || HG</award-id></award-group><award-group><funding-source country="United States">National Human Genome Research Institute : NHGRI</funding-source><award-id>U54 HG004028-02 || HG</award-id></award-group><award-group><funding-source country="United States">National Human Genome Research Institute : NHGRI</funding-source><award-id>U54 HG004028-01 || HG</award-id></award-group></funding-group></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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