Semantically enabling pharmacogenomic data for the realization of personalized medicine

Abstract

Understanding how each individual's genetics and physiology influences pharmaceutical response is crucial to the realization of personalized medicine and the discovery and validation of pharmacogenomic biomarkers is key to its success. However, integration of genotype and phenotype knowledge in medical information systems remains a critical challenge. The inability to easily and accurately integrate the results of biomolecular studies with patients' medical records and clinical reports prevents us from realizing the full potential of pharmacogenomic knowledge for both drug development and clinical practice. Herein, we describe approaches using Semantic Web technologies, in which pharmacogenomic knowledge relevant to drug development and medical decision support is represented in such a way that it can be efficiently accessed both by software and human experts. We suggest that this approach increases the utility of data, and that such computational technologies will become an essential part of personalized medicine, alongside diagnostics and pharmaceutical products.

Figure 1. The components of an IT infrastructure for personalized pharmacotherapy

Relevant datasets such as genotype–phenotype associations or information about specific drugs are exposed publicly on the World Wide Web in Semantic Web formats. The datasets are interlinked, forming a distributed, yet coherent knowledge base. This knowledge base can then be used as the basis for the creation of clinical decision support systems, which can reason over individual patient data when medical professionals are prescribing drugs.

Figure 2. Web Ontology Language can be used to describe groups and subgroups of patients with specific pharmacogenomic needs

Based on molecular data and basic clinical data, a Web Ontology Language reasoner can automatically classify patients into the appropriate pharmacogenomic groups. A decision support application can then provide medical professionals with alerts, reminders and recommendations for each specific patient group.