AlzPharm: integration of neurodegeneration data using RDF
Identifieur interne : 000032 ( Ncbi/Merge ); précédent : 000031; suivant : 000033AlzPharm: integration of neurodegeneration data using RDF
Auteurs : Hugo Yk Lam [États-Unis] ; Luis Marenco [États-Unis] ; Tim Clark [États-Unis] ; Yong Gao [États-Unis] ; June Kinoshita ; Gordon Shepherd [États-Unis] ; Perry Miller [États-Unis] ; Elizabeth Wu ; Gwendolyn T. Wong ; Nian Liu [États-Unis] ; Chiquito Crasto [États-Unis] ; Thomas Morse [États-Unis] ; Susie Stephens [États-Unis] ; Kei-Hoi Cheung [États-Unis]Source :
- BMC Bioinformatics [ 1471-2105 ] ; 2007.
Abstract
Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering complex neuroscience research questions. Domain ontologies can enable the querying heterogeneous data sets, but they are not sufficient for neuroscience since the data of interest commonly span multiple research domains. To this end, e-Neuroscience seeks to provide an integrated platform for neuroscientists to discover new knowledge through seamless integration of the very diverse types of neuroscience data. Here we present a Semantic Web approach to building this e-Neuroscience framework by using the Resource Description Framework (RDF) and its vocabulary description language, RDF Schema (RDFS), as a standard data model to facilitate both representation and integration of the data.
We have constructed a pilot ontology for BrainPharm (a subset of SenseLab) using RDFS and then converted a subset of the BrainPharm data into RDF according to the ontological structure. We have also integrated the converted BrainPharm data with existing RDF hypothesis and publication data from a pilot version of SWAN (Semantic Web Applications in Neuromedicine). Our implementation uses the RDF Data Model in Oracle Database 10g release 2 for data integration, query, and inference, while our Web interface allows users to query the data and retrieve the results in a convenient fashion.
Accessing and integrating biomedical data which cuts across multiple disciplines will be increasingly indispensable and beneficial to neuroscience researchers. The Semantic Web approach we undertook has demonstrated a promising way to semantically integrate data sets created independently. It also shows how advanced queries and inferences can be performed over the integrated data, which are hard to achieve using traditional data integration approaches. Our pilot results suggest that our Semantic Web approach is suitable for realizing e-Neuroscience and generic enough to be applied in other biomedical fields.
Url:
DOI: 10.1186/1471-2105-8-S3-S4
PubMed: 17493287
PubMed Central: 1892101
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PMC:1892101Le document en format XML
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<series><title level="j">BMC Bioinformatics</title>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering complex neuroscience research questions. Domain ontologies can enable the querying heterogeneous data sets, but they are not sufficient for neuroscience since the data of interest commonly span multiple research domains. To this end, e-Neuroscience seeks to provide an integrated platform for neuroscientists to discover new knowledge through seamless integration of the very diverse types of neuroscience data. Here we present a Semantic Web approach to building this e-Neuroscience framework by using the Resource Description Framework (RDF) and its vocabulary description language, RDF Schema (RDFS), as a standard data model to facilitate both representation and integration of the data.</p>
</sec>
<sec><title>Results</title>
<p>We have constructed a pilot ontology for BrainPharm (a subset of SenseLab) using RDFS and then converted a subset of the BrainPharm data into RDF according to the ontological structure. We have also integrated the converted BrainPharm data with existing RDF hypothesis and publication data from a pilot version of SWAN (Semantic Web Applications in Neuromedicine). Our implementation uses the RDF Data Model in Oracle Database 10g release 2 for data integration, query, and inference, while our Web interface allows users to query the data and retrieve the results in a convenient fashion.</p>
</sec>
<sec><title>Conclusion</title>
<p>Accessing and integrating biomedical data which cuts across multiple disciplines will be increasingly indispensable and beneficial to neuroscience researchers. The Semantic Web approach we undertook has demonstrated a promising way to semantically integrate data sets created independently. It also shows how advanced queries and inferences can be performed over the integrated data, which are hard to achieve using traditional data integration approaches. Our pilot results suggest that our Semantic Web approach is suitable for realizing e-Neuroscience and generic enough to be applied in other biomedical fields.</p>
</sec>
</div>
</front>
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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">BMC Bioinformatics</journal-id>
<journal-title>BMC Bioinformatics</journal-title>
<issn pub-type="epub">1471-2105</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
<publisher-loc>London</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">17493287</article-id>
<article-id pub-id-type="pmc">1892101</article-id>
<article-id pub-id-type="publisher-id">1471-2105-8-S3-S4</article-id>
<article-id pub-id-type="doi">10.1186/1471-2105-8-S3-S4</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research</subject>
</subj-group>
</article-categories>
<title-group><article-title>AlzPharm: integration of neurodegeneration data using RDF</article-title>
</title-group>
<contrib-group><contrib id="A1" contrib-type="author"><name><surname>Lam</surname>
<given-names>Hugo YK</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>Hugo.YK.Lam@yale.edu</email>
</contrib>
<contrib id="A2" contrib-type="author"><name><surname>Marenco</surname>
<given-names>Luis</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<xref ref-type="aff" rid="I3">3</xref>
<email>Luis.Marenco@yale.edu</email>
</contrib>
<contrib id="A3" contrib-type="author"><name><surname>Clark</surname>
<given-names>Tim</given-names>
</name>
<xref ref-type="aff" rid="I8">8</xref>
<xref ref-type="aff" rid="I9">9</xref>
<email>Tim_Clark@harvard.edu</email>
</contrib>
<contrib id="A4" contrib-type="author"><name><surname>Gao</surname>
<given-names>Yong</given-names>
</name>
<xref ref-type="aff" rid="I9">9</xref>
<email>YGao@partners.org</email>
</contrib>
<contrib id="A5" contrib-type="author"><name><surname>Kinoshita</surname>
<given-names>June</given-names>
</name>
<xref ref-type="aff" rid="I10">10</xref>
<email>JuneKino@alzforum.org</email>
</contrib>
<contrib id="A6" contrib-type="author"><name><surname>Shepherd</surname>
<given-names>Gordon</given-names>
</name>
<xref ref-type="aff" rid="I4">4</xref>
<email>Gordon.Shepherd@yale.edu</email>
</contrib>
<contrib id="A7" contrib-type="author"><name><surname>Miller</surname>
<given-names>Perry</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<xref ref-type="aff" rid="I3">3</xref>
<xref ref-type="aff" rid="I5">5</xref>
<email>Perry.Miller@yale.edu</email>
</contrib>
<contrib id="A8" contrib-type="author"><name><surname>Wu</surname>
<given-names>Elizabeth</given-names>
</name>
<xref ref-type="aff" rid="I10">10</xref>
<email>Ewu@alzforum.org</email>
</contrib>
<contrib id="A9" contrib-type="author"><name><surname>Wong</surname>
<given-names>Gwendolyn T</given-names>
</name>
<xref ref-type="aff" rid="I10">10</xref>
<email>Wonglabow@verizon.net</email>
</contrib>
<contrib id="A10" contrib-type="author"><name><surname>Liu</surname>
<given-names>Nian</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<xref ref-type="aff" rid="I3">3</xref>
<email>Nian.Liu@yale.edu</email>
</contrib>
<contrib id="A11" contrib-type="author"><name><surname>Crasto</surname>
<given-names>Chiquito</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<xref ref-type="aff" rid="I4">4</xref>
<email>Chiquito.Crasto@yale.edu</email>
</contrib>
<contrib id="A12" contrib-type="author"><name><surname>Morse</surname>
<given-names>Thomas</given-names>
</name>
<xref ref-type="aff" rid="I4">4</xref>
<email>Tom.Morse@yale.edu</email>
</contrib>
<contrib id="A13" contrib-type="author"><name><surname>Stephens</surname>
<given-names>Susie</given-names>
</name>
<xref ref-type="aff" rid="I11">11</xref>
<email>Susie.Stephens@gmail.com</email>
</contrib>
<contrib id="A14" corresp="yes" contrib-type="author"><name><surname>Cheung</surname>
<given-names>Kei-Hoi</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<xref ref-type="aff" rid="I3">3</xref>
<xref ref-type="aff" rid="I6">6</xref>
<xref ref-type="aff" rid="I7">7</xref>
<email>Kei.Cheung@yale.edu</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA</aff>
<aff id="I2"><label>2</label>
Center for Medical Informatics, Yale University, New Haven, CT, USA</aff>
<aff id="I3"><label>3</label>
Department of Anesthesiology, Yale University, New Haven, CT, USA</aff>
<aff id="I4"><label>4</label>
Department of Neurobiology, Yale University, New Haven, CT, USA</aff>
<aff id="I5"><label>5</label>
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA</aff>
<aff id="I6"><label>6</label>
Department of Genetics, Yale University, New Haven, CT, USA</aff>
<aff id="I7"><label>7</label>
Department of Computer Science, Yale University, New Haven, CT, USA</aff>
<aff id="I8"><label>8</label>
Initiative in Innovative Computing, Harvard University, Cambridge, MA, USA</aff>
<aff id="I9"><label>9</label>
Massachusetts General Hospital, Boston, MA, USA</aff>
<aff id="I10"><label>10</label>
Alzheimer Research Forum</aff>
<aff id="I11"><label>11</label>
Oracle, Burlington, MA, USA</aff>
<pub-date pub-type="collection"><year>2007</year>
</pub-date>
<pub-date pub-type="epub"><day>9</day>
<month>5</month>
<year>2007</year>
</pub-date>
<volume>8</volume>
<issue>Suppl 3</issue>
<supplement><named-content content-type="supplement-title">Semantic e-Science in Biomedicine</named-content>
<named-content content-type="supplement-editor">Yimin Wang, Zhaohui Wu, Huajun Chen</named-content>
</supplement>
<fpage>S4</fpage>
<lpage>S4</lpage>
<ext-link ext-link-type="uri" xlink:href="http://www.biomedcentral.com/1471-2105/8/S3/S4"></ext-link>
<permissions><copyright-statement>Copyright © 2007 Lam et al; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2007</copyright-year>
<copyright-holder>Lam 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>
Lam
YK
Hugo
Hugo.YK.Lam@yale.edu
AlzPharm: integration of neurodegeneration data using RDF
2007 BMC Bioinformatics 8(Suppl 3): S4-. (2007) 1471-2105(2007)8:Suppl 3 urn:ISSN:1471-2105 </pmc-comment>
</license>
</permissions>
<abstract><sec><title>Background</title>
<p>Neuroscientists often need to access a wide range of data sets distributed over the Internet. These data sets, however, are typically neither integrated nor interoperable, resulting in a barrier to answering complex neuroscience research questions. Domain ontologies can enable the querying heterogeneous data sets, but they are not sufficient for neuroscience since the data of interest commonly span multiple research domains. To this end, e-Neuroscience seeks to provide an integrated platform for neuroscientists to discover new knowledge through seamless integration of the very diverse types of neuroscience data. Here we present a Semantic Web approach to building this e-Neuroscience framework by using the Resource Description Framework (RDF) and its vocabulary description language, RDF Schema (RDFS), as a standard data model to facilitate both representation and integration of the data.</p>
</sec>
<sec><title>Results</title>
<p>We have constructed a pilot ontology for BrainPharm (a subset of SenseLab) using RDFS and then converted a subset of the BrainPharm data into RDF according to the ontological structure. We have also integrated the converted BrainPharm data with existing RDF hypothesis and publication data from a pilot version of SWAN (Semantic Web Applications in Neuromedicine). Our implementation uses the RDF Data Model in Oracle Database 10g release 2 for data integration, query, and inference, while our Web interface allows users to query the data and retrieve the results in a convenient fashion.</p>
</sec>
<sec><title>Conclusion</title>
<p>Accessing and integrating biomedical data which cuts across multiple disciplines will be increasingly indispensable and beneficial to neuroscience researchers. The Semantic Web approach we undertook has demonstrated a promising way to semantically integrate data sets created independently. It also shows how advanced queries and inferences can be performed over the integrated data, which are hard to achieve using traditional data integration approaches. Our pilot results suggest that our Semantic Web approach is suitable for realizing e-Neuroscience and generic enough to be applied in other biomedical fields.</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Connecticut</li>
<li>Massachusetts</li>
</region>
<settlement><li>Cambridge (Massachusetts)</li>
</settlement>
<orgName><li>Université Harvard</li>
</orgName>
</list>
<tree><noCountry><name sortKey="Kinoshita, June" sort="Kinoshita, June" uniqKey="Kinoshita J" first="June" last="Kinoshita">June Kinoshita</name>
<name sortKey="Wong, Gwendolyn T" sort="Wong, Gwendolyn T" uniqKey="Wong G" first="Gwendolyn T" last="Wong">Gwendolyn T. Wong</name>
<name sortKey="Wu, Elizabeth" sort="Wu, Elizabeth" uniqKey="Wu E" first="Elizabeth" last="Wu">Elizabeth Wu</name>
</noCountry>
<country name="États-Unis"><region name="Connecticut"><name sortKey="Lam, Hugo Yk" sort="Lam, Hugo Yk" uniqKey="Lam H" first="Hugo Yk" last="Lam">Hugo Yk Lam</name>
</region>
<name sortKey="Cheung, Kei Hoi" sort="Cheung, Kei Hoi" uniqKey="Cheung K" first="Kei-Hoi" last="Cheung">Kei-Hoi Cheung</name>
<name sortKey="Cheung, Kei Hoi" sort="Cheung, Kei Hoi" uniqKey="Cheung K" first="Kei-Hoi" last="Cheung">Kei-Hoi Cheung</name>
<name sortKey="Cheung, Kei Hoi" sort="Cheung, Kei Hoi" uniqKey="Cheung K" first="Kei-Hoi" last="Cheung">Kei-Hoi Cheung</name>
<name sortKey="Cheung, Kei Hoi" sort="Cheung, Kei Hoi" uniqKey="Cheung K" first="Kei-Hoi" last="Cheung">Kei-Hoi Cheung</name>
<name sortKey="Clark, Tim" sort="Clark, Tim" uniqKey="Clark T" first="Tim" last="Clark">Tim Clark</name>
<name sortKey="Clark, Tim" sort="Clark, Tim" uniqKey="Clark T" first="Tim" last="Clark">Tim Clark</name>
<name sortKey="Crasto, Chiquito" sort="Crasto, Chiquito" uniqKey="Crasto C" first="Chiquito" last="Crasto">Chiquito Crasto</name>
<name sortKey="Crasto, Chiquito" sort="Crasto, Chiquito" uniqKey="Crasto C" first="Chiquito" last="Crasto">Chiquito Crasto</name>
<name sortKey="Gao, Yong" sort="Gao, Yong" uniqKey="Gao Y" first="Yong" last="Gao">Yong Gao</name>
<name sortKey="Liu, Nian" sort="Liu, Nian" uniqKey="Liu N" first="Nian" last="Liu">Nian Liu</name>
<name sortKey="Liu, Nian" sort="Liu, Nian" uniqKey="Liu N" first="Nian" last="Liu">Nian Liu</name>
<name sortKey="Marenco, Luis" sort="Marenco, Luis" uniqKey="Marenco L" first="Luis" last="Marenco">Luis Marenco</name>
<name sortKey="Marenco, Luis" sort="Marenco, Luis" uniqKey="Marenco L" first="Luis" last="Marenco">Luis Marenco</name>
<name sortKey="Miller, Perry" sort="Miller, Perry" uniqKey="Miller P" first="Perry" last="Miller">Perry Miller</name>
<name sortKey="Miller, Perry" sort="Miller, Perry" uniqKey="Miller P" first="Perry" last="Miller">Perry Miller</name>
<name sortKey="Miller, Perry" sort="Miller, Perry" uniqKey="Miller P" first="Perry" last="Miller">Perry Miller</name>
<name sortKey="Morse, Thomas" sort="Morse, Thomas" uniqKey="Morse T" first="Thomas" last="Morse">Thomas Morse</name>
<name sortKey="Shepherd, Gordon" sort="Shepherd, Gordon" uniqKey="Shepherd G" first="Gordon" last="Shepherd">Gordon Shepherd</name>
<name sortKey="Stephens, Susie" sort="Stephens, Susie" uniqKey="Stephens S" first="Susie" last="Stephens">Susie Stephens</name>
</country>
</tree>
</affiliations>
</record>
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