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Despite the great interest of using genomics in clinical practice, many obstacles lie in the way of integrating genomic and personalized medicine into routine clinical care. Extended to genomic and personalized medicine, clinical decision support system (CDSS) could support the consistent and evidence-based application of genetic and genomic information in healthcare in many ways. In this paper we describe a CDSS designed to assist physicians for personalized care, and methodology for integration in the clinical workflow. A reasoning method for interacting heterogeneous knowledge and data is a necessity in the context of personalized medicine to achieve its potential and improve the quality, safety and efficiency of healthcare.