The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside
Identifieur interne : 000647 ( Main/Exploration ); précédent : 000646; suivant : 000648The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside
Auteurs : Joanne S. Luciano [États-Unis] ; Bosse Andersson [Suède] ; Colin Batchelor [Royaume-Uni] ; Olivier Bodenreider [États-Unis] ; Tim Clark [États-Unis] ; Christine K. Denney [États-Unis] ; Christopher Domarew [États-Unis] ; Thomas Gambet [États-Unis] ; Lee Harland [Royaume-Uni] ; Anja Jentzsch [Allemagne] ; Vipul Kashyap [États-Unis] ; Peter Kos [États-Unis] ; Julia Kozlovsky [États-Unis] ; Timothy Lebo [États-Unis] ; Scott M. Marshall ; James P. Mccusker [États-Unis] ; Deborah L. Mcguinness [États-Unis] ; Chimezie Ogbuji [États-Unis] ; Elgar Pichler [États-Unis] ; Robert L. Powers [États-Unis] ; Eric Prud Ommeaux [États-Unis] ; Matthias Samwald [Autriche, Irlande (pays)] ; Lynn Schriml ; Peter J Tonellato [États-Unis] ; Patricia L Whetzel [États-Unis] ; Jun Zhao [Royaume-Uni] ; Susie Stephens [États-Unis] ; Michel Dumontier [Canada]Source :
- Journal of Biomedical Semantics [ 2041-1480 ] ; 2011.
Abstract
Translational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medicine Knowledge Base (TMKB) capable of answering questions relating to clinical practice and pharmaceutical drug discovery.
We developed the Translational Medicine Ontology (TMO) as a unifying ontology to integrate chemical, genomic and proteomic data with disease, treatment, and electronic health records. We demonstrate the use of Semantic Web technologies in the integration of patient and biomedical data, and reveal how such a knowledge base can aid physicians in providing tailored patient care and facilitate the recruitment of patients into active clinical trials. Thus, patients, physicians and researchers may explore the knowledge base to better understand therapeutic options, efficacy, and mechanisms of action.
This work takes an important step in using Semantic Web technologies to facilitate integration of relevant, distributed, external sources and progress towards a computational platform to support personalized medicine.
TMO can be downloaded from
Url:
DOI: 10.1186/2041-1480-2-S2-S1
PubMed: 21624155
PubMed Central: 3102889
Affiliations:
- Allemagne, Autriche, Canada, Irlande (pays), Royaume-Uni, Suède, États-Unis
- Angleterre, Berlin, Californie, Connecticut, Indiana, Maryland, Massachusetts, Ohio, Oxfordshire, Pennsylvanie, Vienne (Autriche), État de New York
- Berlin, Oxford, Vienne (Autriche)
- Université d'Oxford
Links toward previous steps (curation, corpus...)
- to stream Pmc, to step Corpus: 000551
- to stream Pmc, to step Curation: 000551
- to stream Pmc, to step Checkpoint: 000468
- to stream Ncbi, to step Merge: 000232
- to stream Ncbi, to step Curation: 000232
- to stream Ncbi, to step Checkpoint: 000232
- to stream Main, to step Merge: 000649
- to stream Main, to step Curation: 000647
Le document en format XML
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Powers</name><affiliation wicri:level="2"><nlm:aff id="I2">Predictive Medicine Inc., Belmont, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Predictive Medicine Inc., Belmont, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Prud Ommeaux, Eric" sort="Prud Ommeaux, Eric" uniqKey="Prud Ommeaux E" first="Eric" last="Prud Ommeaux">Eric Prud Ommeaux</name><affiliation wicri:level="2"><nlm:aff id="I10">W3C, Cambridge, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>W3C, Cambridge, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Samwald, Matthias" sort="Samwald, Matthias" uniqKey="Samwald M" first="Matthias" last="Samwald">Matthias Samwald</name><affiliation wicri:level="3"><nlm:aff id="I19">Medical University of Vienna, Vienna, Austria</nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Medical University of Vienna, Vienna</wicri:regionArea><placeName><settlement type="city">Vienne (Autriche)</settlement><region nuts="2" type="province">Vienne (Autriche)</region></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="I20">Information Retrieval Facility (IRF), Vienna, Austria</nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Information Retrieval Facility (IRF), Vienna</wicri:regionArea><placeName><settlement type="city">Vienne (Autriche)</settlement><region nuts="2" type="province">Vienne (Autriche)</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="I21">Digital Enterprise Research Institute (DERI), National University of Ireland Galway, Ireland</nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>Digital Enterprise Research Institute (DERI), National University of Ireland Galway</wicri:regionArea><wicri:noRegion>National University of Ireland Galway</wicri:noRegion></affiliation></author><author><name sortKey="Schriml, Lynn" sort="Schriml, Lynn" uniqKey="Schriml L" first="Lynn" last="Schriml">Lynn Schriml</name><affiliation><nlm:aff id="I22">University of Maryland, Institute for Genome Sciences</nlm:aff><wicri:noCountry code="subfield">Institute for Genome Sciences</wicri:noCountry></affiliation></author><author><name sortKey="Tonellato, Peter J" sort="Tonellato, Peter J" uniqKey="Tonellato P" first="Peter J" last="Tonellato">Peter J Tonellato</name><affiliation wicri:level="2"><nlm:aff id="I6">Harvard Medical School, Boston, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Harvard Medical School, Boston, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Whetzel, Patricia L" sort="Whetzel, Patricia L" uniqKey="Whetzel P" first="Patricia L" last="Whetzel">Patricia L Whetzel</name><affiliation wicri:level="2"><nlm:aff id="I23">Stanford University, Stanford, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Zhao, Jun" sort="Zhao, Jun" uniqKey="Zhao J" first="Jun" last="Zhao">Jun Zhao</name><affiliation wicri:level="4"><nlm:aff id="I24">University of Oxford, Oxford, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>University of Oxford, Oxford</wicri:regionArea><placeName><settlement type="city">Oxford</settlement><region type="country">Angleterre</region><region type="comté" nuts="2">Oxfordshire</region></placeName><orgName type="university">Université d'Oxford</orgName></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="I25">Johnson & Johnson Pharmaceutical Research & Development L.L.C., Radnor, PA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Johnson & Johnson Pharmaceutical Research & Development L.L.C., Radnor, PA</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author><author><name sortKey="Dumontier, Michel" sort="Dumontier, Michel" uniqKey="Dumontier M" first="Michel" last="Dumontier">Michel Dumontier</name><affiliation wicri:level="1"><nlm:aff id="I26">Carleton University, Ottawa, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Carleton University, Ottawa</wicri:regionArea><wicri:noRegion>Ottawa</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21624155</idno><idno type="pmc">3102889</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102889</idno><idno type="RBID">PMC:3102889</idno><idno type="doi">10.1186/2041-1480-2-S2-S1</idno><date when="2011">2011</date><idno type="wicri:Area/Pmc/Corpus">000551</idno><idno type="wicri:Area/Pmc/Curation">000551</idno><idno type="wicri:Area/Pmc/Checkpoint">000468</idno><idno type="wicri:Area/Ncbi/Merge">000232</idno><idno type="wicri:Area/Ncbi/Curation">000232</idno><idno type="wicri:Area/Ncbi/Checkpoint">000232</idno><idno type="wicri:Area/Main/Merge">000649</idno><idno type="wicri:Area/Main/Curation">000647</idno><idno type="wicri:Area/Main/Exploration">000647</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside</title><author><name sortKey="Luciano, Joanne S" sort="Luciano, Joanne S" uniqKey="Luciano J" first="Joanne S" last="Luciano">Joanne S. Luciano</name><affiliation wicri:level="2"><nlm:aff id="I1">Rensselaer Polytechnic Institute, Troy, NY, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Rensselaer Polytechnic Institute, Troy, NY</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Predictive Medicine Inc., Belmont, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Predictive Medicine Inc., Belmont, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Andersson, Bosse" sort="Andersson, Bosse" uniqKey="Andersson B" first="Bosse" last="Andersson">Bosse Andersson</name><affiliation wicri:level="1"><nlm:aff id="I3">AstraZeneca, Lund, Sweden</nlm:aff><country xml:lang="fr">Suède</country><wicri:regionArea>AstraZeneca, Lund</wicri:regionArea><wicri:noRegion>Lund</wicri:noRegion></affiliation></author><author><name sortKey="Batchelor, Colin" sort="Batchelor, Colin" uniqKey="Batchelor C" first="Colin" last="Batchelor">Colin Batchelor</name><affiliation wicri:level="1"><nlm:aff id="I4">Royal Society of Chemistry, Cambridge, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Royal Society of Chemistry, Cambridge</wicri:regionArea><wicri:noRegion>Cambridge</wicri:noRegion></affiliation></author><author><name sortKey="Bodenreider, Olivier" sort="Bodenreider, Olivier" uniqKey="Bodenreider O" first="Olivier" last="Bodenreider">Olivier Bodenreider</name><affiliation wicri:level="2"><nlm:aff id="I5">National Library of Medicine, Bethesda, MD, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>National Library of Medicine, Bethesda, MD</wicri:regionArea><placeName><region type="state">Maryland</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="2"><nlm:aff id="I6">Harvard Medical School, Boston, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Harvard Medical School, Boston, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation><affiliation><nlm:aff id="I7">University of Manchester, Manchester UK</nlm:aff><wicri:noCountry code="subfield">Manchester UK</wicri:noCountry></affiliation></author><author><name sortKey="Denney, Christine K" sort="Denney, Christine K" uniqKey="Denney C" first="Christine K" last="Denney">Christine K. Denney</name><affiliation wicri:level="2"><nlm:aff id="I8">Eli Lilly and Company, Indianapolis, IN, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Eli Lilly and Company, Indianapolis, IN</wicri:regionArea><placeName><region type="state">Indiana</region></placeName></affiliation></author><author><name sortKey="Domarew, Christopher" sort="Domarew, Christopher" uniqKey="Domarew C" first="Christopher" last="Domarew">Christopher Domarew</name><affiliation wicri:level="2"><nlm:aff id="I9">Albany Medical Center, Albany, NY, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Albany Medical Center, Albany, NY</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Gambet, Thomas" sort="Gambet, Thomas" uniqKey="Gambet T" first="Thomas" last="Gambet">Thomas Gambet</name><affiliation wicri:level="2"><nlm:aff id="I10">W3C, Cambridge, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>W3C, Cambridge, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Harland, Lee" sort="Harland, Lee" uniqKey="Harland L" first="Lee" last="Harland">Lee Harland</name><affiliation wicri:level="1"><nlm:aff id="I11">Pfizer, Sandwich, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>Pfizer, Sandwich</wicri:regionArea><wicri:noRegion>Sandwich</wicri:noRegion></affiliation></author><author><name sortKey="Jentzsch, Anja" sort="Jentzsch, Anja" uniqKey="Jentzsch A" first="Anja" last="Jentzsch">Anja Jentzsch</name><affiliation wicri:level="3"><nlm:aff id="I12">Freie Universität, Berlin, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Freie Universität, Berlin</wicri:regionArea><placeName><region type="land" nuts="3">Berlin</region><settlement type="city">Berlin</settlement></placeName></affiliation></author><author><name sortKey="Kashyap, Vipul" sort="Kashyap, Vipul" uniqKey="Kashyap V" first="Vipul" last="Kashyap">Vipul Kashyap</name><affiliation wicri:level="2"><nlm:aff id="I13">Cigna, Hartford, CT, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Cigna, Hartford, CT</wicri:regionArea><placeName><region type="state">Connecticut</region></placeName></affiliation></author><author><name sortKey="Kos, Peter" sort="Kos, Peter" uniqKey="Kos P" first="Peter" last="Kos">Peter Kos</name><affiliation wicri:level="2"><nlm:aff id="I6">Harvard Medical School, Boston, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Harvard Medical School, Boston, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Kozlovsky, Julia" sort="Kozlovsky, Julia" uniqKey="Kozlovsky J" first="Julia" last="Kozlovsky">Julia Kozlovsky</name><affiliation wicri:level="2"><nlm:aff id="I14">AstraZeneca, Waltham, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>AstraZeneca, Waltham, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Lebo, Timothy" sort="Lebo, Timothy" uniqKey="Lebo T" first="Timothy" last="Lebo">Timothy Lebo</name><affiliation wicri:level="2"><nlm:aff id="I1">Rensselaer Polytechnic Institute, Troy, NY, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Rensselaer Polytechnic Institute, Troy, NY</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Marshall, Scott M" sort="Marshall, Scott M" uniqKey="Marshall S" first="Scott M" last="Marshall">Scott M. Marshall</name><affiliation><nlm:aff id="I15">Leiden University Medical Center, Leiden, NL</nlm:aff><wicri:noCountry code="subfield">NL</wicri:noCountry></affiliation><affiliation><nlm:aff id="I16">University of Amsterdam, Amsterdam, NL</nlm:aff><wicri:noCountry code="subfield">NL</wicri:noCountry></affiliation></author><author><name sortKey="Mccusker, James P" sort="Mccusker, James P" uniqKey="Mccusker J" first="James P" last="Mccusker">James P. Mccusker</name><affiliation wicri:level="2"><nlm:aff id="I1">Rensselaer Polytechnic Institute, Troy, NY, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Rensselaer Polytechnic Institute, Troy, NY</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Mcguinness, Deborah L" sort="Mcguinness, Deborah L" uniqKey="Mcguinness D" first="Deborah L" last="Mcguinness">Deborah L. Mcguinness</name><affiliation wicri:level="2"><nlm:aff id="I1">Rensselaer Polytechnic Institute, Troy, NY, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Rensselaer Polytechnic Institute, Troy, NY</wicri:regionArea><placeName><region type="state">État de New York</region></placeName></affiliation></author><author><name sortKey="Ogbuji, Chimezie" sort="Ogbuji, Chimezie" uniqKey="Ogbuji C" first="Chimezie" last="Ogbuji">Chimezie Ogbuji</name><affiliation wicri:level="2"><nlm:aff id="I17">Case Western Reserve University School of Medicine, Cleveland, OH, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Case Western Reserve University School of Medicine, Cleveland, OH</wicri:regionArea><placeName><region type="state">Ohio</region></placeName></affiliation></author><author><name sortKey="Pichler, Elgar" sort="Pichler, Elgar" uniqKey="Pichler E" first="Elgar" last="Pichler">Elgar Pichler</name><affiliation wicri:level="2"><nlm:aff id="I18">W3C HCLSIG, W3C, Cambridge, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>W3C HCLSIG, W3C, Cambridge, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Powers, Robert L" sort="Powers, Robert L" uniqKey="Powers R" first="Robert L" last="Powers">Robert L. Powers</name><affiliation wicri:level="2"><nlm:aff id="I2">Predictive Medicine Inc., Belmont, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Predictive Medicine Inc., Belmont, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Prud Ommeaux, Eric" sort="Prud Ommeaux, Eric" uniqKey="Prud Ommeaux E" first="Eric" last="Prud Ommeaux">Eric Prud Ommeaux</name><affiliation wicri:level="2"><nlm:aff id="I10">W3C, Cambridge, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>W3C, Cambridge, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Samwald, Matthias" sort="Samwald, Matthias" uniqKey="Samwald M" first="Matthias" last="Samwald">Matthias Samwald</name><affiliation wicri:level="3"><nlm:aff id="I19">Medical University of Vienna, Vienna, Austria</nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Medical University of Vienna, Vienna</wicri:regionArea><placeName><settlement type="city">Vienne (Autriche)</settlement><region nuts="2" type="province">Vienne (Autriche)</region></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="I20">Information Retrieval Facility (IRF), Vienna, Austria</nlm:aff><country xml:lang="fr">Autriche</country><wicri:regionArea>Information Retrieval Facility (IRF), Vienna</wicri:regionArea><placeName><settlement type="city">Vienne (Autriche)</settlement><region nuts="2" type="province">Vienne (Autriche)</region></placeName></affiliation><affiliation wicri:level="1"><nlm:aff id="I21">Digital Enterprise Research Institute (DERI), National University of Ireland Galway, Ireland</nlm:aff><country xml:lang="fr">Irlande (pays)</country><wicri:regionArea>Digital Enterprise Research Institute (DERI), National University of Ireland Galway</wicri:regionArea><wicri:noRegion>National University of Ireland Galway</wicri:noRegion></affiliation></author><author><name sortKey="Schriml, Lynn" sort="Schriml, Lynn" uniqKey="Schriml L" first="Lynn" last="Schriml">Lynn Schriml</name><affiliation><nlm:aff id="I22">University of Maryland, Institute for Genome Sciences</nlm:aff><wicri:noCountry code="subfield">Institute for Genome Sciences</wicri:noCountry></affiliation></author><author><name sortKey="Tonellato, Peter J" sort="Tonellato, Peter J" uniqKey="Tonellato P" first="Peter J" last="Tonellato">Peter J Tonellato</name><affiliation wicri:level="2"><nlm:aff id="I6">Harvard Medical School, Boston, MA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Harvard Medical School, Boston, MA</wicri:regionArea><placeName><region type="state">Massachusetts</region></placeName></affiliation></author><author><name sortKey="Whetzel, Patricia L" sort="Whetzel, Patricia L" uniqKey="Whetzel P" first="Patricia L" last="Whetzel">Patricia L Whetzel</name><affiliation wicri:level="2"><nlm:aff id="I23">Stanford University, Stanford, CA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Stanford University, Stanford, CA</wicri:regionArea><placeName><region type="state">Californie</region></placeName></affiliation></author><author><name sortKey="Zhao, Jun" sort="Zhao, Jun" uniqKey="Zhao J" first="Jun" last="Zhao">Jun Zhao</name><affiliation wicri:level="4"><nlm:aff id="I24">University of Oxford, Oxford, UK</nlm:aff><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>University of Oxford, Oxford</wicri:regionArea><placeName><settlement type="city">Oxford</settlement><region type="country">Angleterre</region><region type="comté" nuts="2">Oxfordshire</region></placeName><orgName type="university">Université d'Oxford</orgName></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="I25">Johnson & Johnson Pharmaceutical Research & Development L.L.C., Radnor, PA, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Johnson & Johnson Pharmaceutical Research & Development L.L.C., Radnor, PA</wicri:regionArea><placeName><region type="state">Pennsylvanie</region></placeName></affiliation></author><author><name sortKey="Dumontier, Michel" sort="Dumontier, Michel" uniqKey="Dumontier M" first="Michel" last="Dumontier">Michel Dumontier</name><affiliation wicri:level="1"><nlm:aff id="I26">Carleton University, Ottawa, Canada</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Carleton University, Ottawa</wicri:regionArea><wicri:noRegion>Ottawa</wicri:noRegion></affiliation></author></analytic><series><title level="j">Journal of Biomedical Semantics</title><idno type="eISSN">2041-1480</idno><imprint><date when="2011">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><sec><title>Background</title><p>Translational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medicine Knowledge Base (TMKB) capable of answering questions relating to clinical practice and pharmaceutical drug discovery.</p></sec><sec><title>Results</title><p>We developed the Translational Medicine Ontology (TMO) as a unifying ontology to integrate chemical, genomic and proteomic data with disease, treatment, and electronic health records. We demonstrate the use of Semantic Web technologies in the integration of patient and biomedical data, and reveal how such a knowledge base can aid physicians in providing tailored patient care and facilitate the recruitment of patients into active clinical trials. Thus, patients, physicians and researchers may explore the knowledge base to better understand therapeutic options, efficacy, and mechanisms of action.</p></sec><sec><title>Conclusions</title><p>This work takes an important step in using Semantic Web technologies to facilitate integration of relevant, distributed, external sources and progress towards a computational platform to support personalized medicine.</p></sec><sec><title>Availability</title><p>TMO can be downloaded from <ext-link ext-link-type="uri" xlink:href="http://code.google.com/p/translationalmedicineontology">http://code.google.com/p/translationalmedicineontology</ext-link> and TMKB can be accessed at <ext-link ext-link-type="uri" xlink:href="http://tm.semanticscience.org/sparql">http://tm.semanticscience.org/sparql</ext-link>.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Trusheim, M" uniqKey="Trusheim M">M Trusheim</name></author><author><name 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uniqKey="Luciano J">JS Luciano</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Levine, M" uniqKey="Levine M">M Levine</name></author><author><name sortKey="Calvanio, R" uniqKey="Calvanio R">R Calvanio</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Calvanio, R" uniqKey="Calvanio R">R Calvanio</name></author><author><name sortKey="Buonanno, F" uniqKey="Buonanno F">F Buonanno</name></author><author><name sortKey="Levine, D" uniqKey="Levine D">D Levine</name></author><author><name sortKey="Levine, M" uniqKey="Levine M">M Levine</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Allemang, D" uniqKey="Allemang D">D Allemang</name></author><author><name sortKey="Hendler, J" uniqKey="Hendler J">J Hendler</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Deus, H" uniqKey="Deus H">H Deus</name></author><author><name sortKey="Zhao, J" 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uniqKey="Greenhalgh C">C Greenhalgh</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Allemagne</li><li>Autriche</li><li>Canada</li><li>Irlande (pays)</li><li>Royaume-Uni</li><li>Suède</li><li>États-Unis</li></country><region><li>Angleterre</li><li>Berlin</li><li>Californie</li><li>Connecticut</li><li>Indiana</li><li>Maryland</li><li>Massachusetts</li><li>Ohio</li><li>Oxfordshire</li><li>Pennsylvanie</li><li>Vienne (Autriche)</li><li>État de New York</li></region><settlement><li>Berlin</li><li>Oxford</li><li>Vienne (Autriche)</li></settlement><orgName><li>Université d'Oxford</li></orgName></list><tree><noCountry><name sortKey="Marshall, Scott M" sort="Marshall, Scott M" uniqKey="Marshall S" first="Scott M" last="Marshall">Scott M. Marshall</name><name sortKey="Schriml, Lynn" sort="Schriml, Lynn" uniqKey="Schriml L" first="Lynn" last="Schriml">Lynn Schriml</name></noCountry><country name="États-Unis"><region name="État de New York"><name sortKey="Luciano, Joanne S" sort="Luciano, Joanne S" uniqKey="Luciano J" first="Joanne S" last="Luciano">Joanne S. Luciano</name></region><name sortKey="Bodenreider, Olivier" sort="Bodenreider, Olivier" uniqKey="Bodenreider O" first="Olivier" last="Bodenreider">Olivier Bodenreider</name><name sortKey="Clark, Tim" sort="Clark, Tim" uniqKey="Clark T" first="Tim" last="Clark">Tim Clark</name><name sortKey="Denney, Christine K" sort="Denney, Christine K" uniqKey="Denney C" first="Christine K" last="Denney">Christine K. Denney</name><name sortKey="Domarew, Christopher" sort="Domarew, Christopher" uniqKey="Domarew C" first="Christopher" last="Domarew">Christopher Domarew</name><name sortKey="Gambet, Thomas" sort="Gambet, Thomas" uniqKey="Gambet T" first="Thomas" last="Gambet">Thomas Gambet</name><name sortKey="Kashyap, Vipul" sort="Kashyap, Vipul" uniqKey="Kashyap V" first="Vipul" last="Kashyap">Vipul Kashyap</name><name sortKey="Kos, Peter" sort="Kos, Peter" uniqKey="Kos P" first="Peter" last="Kos">Peter Kos</name><name sortKey="Kozlovsky, Julia" sort="Kozlovsky, Julia" uniqKey="Kozlovsky J" first="Julia" last="Kozlovsky">Julia Kozlovsky</name><name sortKey="Lebo, Timothy" sort="Lebo, Timothy" uniqKey="Lebo T" first="Timothy" last="Lebo">Timothy Lebo</name><name sortKey="Luciano, Joanne S" sort="Luciano, Joanne S" uniqKey="Luciano J" first="Joanne S" last="Luciano">Joanne S. Luciano</name><name sortKey="Mccusker, James P" sort="Mccusker, James P" uniqKey="Mccusker J" first="James P" last="Mccusker">James P. Mccusker</name><name sortKey="Mcguinness, Deborah L" sort="Mcguinness, Deborah L" uniqKey="Mcguinness D" first="Deborah L" last="Mcguinness">Deborah L. Mcguinness</name><name sortKey="Ogbuji, Chimezie" sort="Ogbuji, Chimezie" uniqKey="Ogbuji C" first="Chimezie" last="Ogbuji">Chimezie Ogbuji</name><name sortKey="Pichler, Elgar" sort="Pichler, Elgar" uniqKey="Pichler E" first="Elgar" last="Pichler">Elgar Pichler</name><name sortKey="Powers, Robert L" sort="Powers, Robert L" uniqKey="Powers R" first="Robert L" last="Powers">Robert L. Powers</name><name sortKey="Prud Ommeaux, Eric" sort="Prud Ommeaux, Eric" uniqKey="Prud Ommeaux E" first="Eric" last="Prud Ommeaux">Eric Prud Ommeaux</name><name sortKey="Stephens, Susie" sort="Stephens, Susie" uniqKey="Stephens S" first="Susie" last="Stephens">Susie Stephens</name><name sortKey="Tonellato, Peter J" sort="Tonellato, Peter J" uniqKey="Tonellato P" first="Peter J" last="Tonellato">Peter J Tonellato</name><name sortKey="Whetzel, Patricia L" sort="Whetzel, Patricia L" uniqKey="Whetzel P" first="Patricia L" last="Whetzel">Patricia L Whetzel</name></country><country name="Suède"><noRegion><name sortKey="Andersson, Bosse" sort="Andersson, Bosse" uniqKey="Andersson B" first="Bosse" last="Andersson">Bosse Andersson</name></noRegion></country><country name="Royaume-Uni"><noRegion><name sortKey="Batchelor, Colin" sort="Batchelor, Colin" uniqKey="Batchelor C" first="Colin" last="Batchelor">Colin Batchelor</name></noRegion><name sortKey="Harland, Lee" sort="Harland, Lee" uniqKey="Harland L" first="Lee" last="Harland">Lee Harland</name><name sortKey="Zhao, Jun" sort="Zhao, Jun" uniqKey="Zhao J" first="Jun" last="Zhao">Jun Zhao</name></country><country name="Allemagne"><region name="Berlin"><name sortKey="Jentzsch, Anja" sort="Jentzsch, Anja" uniqKey="Jentzsch A" first="Anja" last="Jentzsch">Anja Jentzsch</name></region></country><country name="Autriche"><region name="Vienne (Autriche)"><name sortKey="Samwald, Matthias" sort="Samwald, Matthias" uniqKey="Samwald M" first="Matthias" last="Samwald">Matthias Samwald</name></region><name sortKey="Samwald, Matthias" sort="Samwald, Matthias" uniqKey="Samwald M" first="Matthias" last="Samwald">Matthias Samwald</name></country><country name="Irlande (pays)"><noRegion><name sortKey="Samwald, Matthias" sort="Samwald, Matthias" uniqKey="Samwald M" first="Matthias" last="Samwald">Matthias Samwald</name></noRegion></country><country name="Canada"><noRegion><name sortKey="Dumontier, Michel" sort="Dumontier, Michel" uniqKey="Dumontier M" first="Michel" last="Dumontier">Michel Dumontier</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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