AlzPharm: integration of neurodegeneration data using RDF
Identifieur interne : 000F04 ( Main/Exploration ); précédent : 000F03; suivant : 000F05AlzPharm: 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
Affiliations:
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type="main">AlzPharm: integration of neurodegeneration data using RDF</title><author><name sortKey="Lam, Hugo Yk" sort="Lam, Hugo Yk" uniqKey="Lam H" first="Hugo Yk" last="Lam">Hugo Yk Lam</name><affiliation wicri:level="2"><nlm:aff id="I1">Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Interdepartmental Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Marenco, Luis" sort="Marenco, Luis" uniqKey="Marenco L" first="Luis" last="Marenco">Luis Marenco</name><affiliation wicri:level="2"><nlm:aff id="I2">Center for Medical Informatics, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Medical Informatics, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Department of Anesthesiology, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Anesthesiology, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Clark, Tim" sort="Clark, Tim" uniqKey="Clark T" first="Tim" last="Clark">Tim Clark</name><affiliation wicri:level="4"><nlm:aff id="I8">Initiative in Innovative Computing, Harvard University, Cambridge, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Initiative in Innovative Computing, Harvard University, Cambridge, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region><settlement type="city">Cambridge (Massachusetts)</settlement></placeName><orgName 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Forum</nlm:aff></affiliation></author><author><name sortKey="Shepherd, Gordon" sort="Shepherd, Gordon" uniqKey="Shepherd G" first="Gordon" last="Shepherd">Gordon Shepherd</name><affiliation wicri:level="2"><nlm:aff id="I4">Department of Neurobiology, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Neurobiology, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Miller, Perry" sort="Miller, Perry" uniqKey="Miller P" first="Perry" last="Miller">Perry Miller</name><affiliation wicri:level="2"><nlm:aff id="I2">Center for Medical Informatics, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Medical Informatics, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Department of Anesthesiology, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Anesthesiology, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I5">Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Wu, Elizabeth" sort="Wu, Elizabeth" uniqKey="Wu E" first="Elizabeth" last="Wu">Elizabeth Wu</name><affiliation><nlm:aff id="I10">Alzheimer Research Forum</nlm:aff></affiliation></author><author><name sortKey="Wong, Gwendolyn T" sort="Wong, Gwendolyn T" uniqKey="Wong G" first="Gwendolyn T" last="Wong">Gwendolyn T. Wong</name><affiliation><nlm:aff id="I10">Alzheimer Research Forum</nlm:aff></affiliation></author><author><name sortKey="Liu, Nian" sort="Liu, Nian" uniqKey="Liu N" first="Nian" last="Liu">Nian Liu</name><affiliation wicri:level="2"><nlm:aff id="I2">Center for Medical Informatics, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Medical Informatics, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Department of Anesthesiology, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Anesthesiology, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Crasto, Chiquito" sort="Crasto, Chiquito" uniqKey="Crasto C" first="Chiquito" last="Crasto">Chiquito Crasto</name><affiliation wicri:level="2"><nlm:aff id="I2">Center for Medical Informatics, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Medical Informatics, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I4">Department of Neurobiology, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Neurobiology, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Morse, Thomas" sort="Morse, Thomas" uniqKey="Morse T" first="Thomas" last="Morse">Thomas Morse</name><affiliation wicri:level="2"><nlm:aff id="I4">Department of Neurobiology, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Neurobiology, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Stephens, Susie" sort="Stephens, Susie" uniqKey="Stephens S" first="Susie" last="Stephens">Susie Stephens</name><affiliation wicri:level="2"><nlm:aff id="I11">Oracle, Burlington, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Oracle, Burlington, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Cheung, Kei Hoi" sort="Cheung, Kei Hoi" uniqKey="Cheung K" first="Kei-Hoi" last="Cheung">Kei-Hoi Cheung</name><affiliation wicri:level="2"><nlm:aff id="I2">Center for Medical Informatics, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Medical Informatics, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Department of Anesthesiology, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Anesthesiology, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I6">Department of Genetics, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Genetics, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I7">Department of Computer Science, Yale University, New Haven, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Yale University, New Haven, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author></analytic><series><title level="j">BMC Bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2007">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><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><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></listBibl></div1></back></TEI><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>Pour manipuler ce document sous Unix (Dilib)
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