The Translational Medicine Ontology and Knowledge Base: Driving personalized medicine by bridging the gap between bench and bedside
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Authors
Luciano, Joanne
Andersson, Bosse
Batchelor, Colin
Bodenreider, Olivier
Clark, Tim
Denney, Christine
Domarew, Christopher
Gambet, Thomas
Harland, Lee
Jentzsch, Anja
Issue Date
2011-05-17
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Abstract
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.
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Publisher
Journal of Biomedical Semantics volume