In post-genome era, the greatest challenge of post-genome research is how we can apply genomic outcome to practical field like clinical medicine through discovering effective findings from its complex and meta-molecular network. From the viewpoint of reducing health care cost, preventive medicine that can avoid diseases should be essential target. Balneology that contains preventive medicine in part through unspecified bio-modulation effect should be a principal field of genome science based application. Balneology has expectations to be applied to practical clinical field or health promotion through translational research to modern medicine or health science. This translational research needs establishment of bridging knowledge and its bi-directional migration as the essence of translation. Integration of in silico knowledge among balneology, modern medicine, and genomic science is the fundamental basis of this translation. Single knowledge architecture that has anatomically hierarchical structure, logical conceptual unit and its supportive evidences makes integration logically seamless and establishes smooth translation. This paper reports knowledge architecture in balneologic translational research and its prototype.