HCLSIG/PharmaOntology/Publications

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TM Publications

2. Joanne S. Luciano, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Tim Clark, Christopher Domarew, Thomas Gambet, Lee Harland, Anja Jentzsch, Vipul Kashyap, Peter Kos , Julia Kozlovsky, M. Scott Marshall, James P. McCusker, Deborah L. McGuinness, James McGurk, Chimezie Ogbuji, Elgar Pichler, Robert L. Powers, Eric Prud'hommeaux, Matthias Samwald, Lynn Schriml, Peter J. Tonellato, Patricia L. Whetzel, Jun Zhao, Michel Dumontier. The Translational Medicine Ontology and Knowledge Base: Driving personalized medicine by bridging the gap between bench and bedside. Special Issue Journal of Biomedical Semantics. in press.

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. A key component of this work is the Translational Medicine Ontology (TMO) which provides a foundation upon which chemical, genomic and proteomic data may be linked to disease, treatments and electronic health records. We demonstrate the use of semantic web technologies in the integration of patient to biomedical data, and how such a knowledge base can aid physicians in providing tailored patient care and facilitate the recruitment of non-responsive 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. The TMKB takes us a step forward in using semantic web technologies to facilitate integration of relevant external sources and we expect this work to form the basis for future work towards the development of a computational platform that supports personalized medicine.

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[Revised (in press) version ]


1. Michel Dumontier, Bosse Andersson, Colin Batchelor, Christine Denney, Christopher Domarew, Anja Jentzsch, Joanne Luciano, Elgar Pichler, Eric Prud'hommeaux, Patricia L. Whetzel, Olivier Bodenreider, Tim Clark, Lee Harland, Vipul Kashyap, Peter Kos, Julia Kozlovsky, James McGurk, Chimezie Ogbuji, Matthias Samwald, Lynn Schriml, Peter J. Tonellato, Jun Zhao, and Susie Stephens. The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to bench. In Proceedings of Bio-ontologies 2010: Semantic Applications in Life Sciences. July 9-10, 2010. Boston, USA.

abstract: The Translational Medicine Ontology provides terminology that bridges diverse areas of translational medicine including hypothesis management, discovery research, drug development and formulation, clinical research, and clinical practice. Designed primarily from use cases, the ontology consists of essential terms that are mapped to other ontologies. It serves as a global schema for data integration while simultaneously facilitating the formulation of complex queries across heterogeneous sources. We demonstrate the utility of the ontology through question answering over a prototype knowledge base composed of sample patient data integrated with linked open data. This work forms a basis for the development of a computational platform for managing information relevant to personalized medicine.

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