TY - JOUR
T1 - The Translational Medicine Ontology and Knowledge Base
T2 - driving personalized medicine by bridging the gap between bench and bedside
AU - Luciano, Joanne S.
AU - Andersson, Bosse
AU - Batchelor, Colin
AU - Bodenreider, Olivier
AU - Clark, Tim
AU - Denney, Christine K
AU - Domarew, Christopher
AU - Gambet, Thomas
AU - Harland, Lee
AU - Jentzsch, Anja
AU - Kashyap, Vipul
AU - Kos, Peter
AU - Kozlovsky, Julia
AU - Lebo, Timothy
AU - Marshall, M Scott
AU - McCusker, James P.
AU - McGuinness, Deborah L.
AU - Ogbuji, Chimezie
AU - Pichler, Elgar
AU - Powers, Robert L.
AU - Prud'hommeaux, Eric
AU - Samwald, Matthias
AU - Schriml, Lynn
AU - Tonellato, Peter J
AU - Whetzel, Patricia L.
AU - Zhao, Jun
AU - Stephens, Susie
AU - Dumontier, Michel
PY - 2011/5/17
Y1 - 2011/5/17
N2 - BACKGROUND: 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.RESULTS: 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.CONCLUSIONS: 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.AVAILABILITY: TMO can be downloaded from http://code.google.com/p/translationalmedicineontology and TMKB can be accessed at http://tm.semanticscience.org/sparql.
AB - BACKGROUND: 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.RESULTS: 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.CONCLUSIONS: 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.AVAILABILITY: TMO can be downloaded from http://code.google.com/p/translationalmedicineontology and TMKB can be accessed at http://tm.semanticscience.org/sparql.
KW - Journal Article
U2 - 10.1186/2041-1480-2-S2-S1
DO - 10.1186/2041-1480-2-S2-S1
M3 - Article
C2 - 21624155
SN - 2041-1480
VL - 2 Suppl 2
SP - S1
JO - Journal of biomedical semantics
JF - Journal of biomedical semantics
ER -