The objective of this paper is to define the basis for the translational research and its knowledge framework in balneology aiming to approach the disease prevention. As a method to attain this objective, we advocate the knowledge framework that can bridge gene ontology (GO), balneologic ontology (BO), and clinical ontology (CO) virtually at a client site with three sided basic concepts as (1) the logically extended anatomical index from micro to macro, (2) the knowledge representation based on feature described logical conceptual unit, and (3) the EBM (Evidence Based Medicine) based quality evaluation of knowledge. As an result, the scheme and the prototype of the knowledge framework for the basic balneology was built. The logically extended anatomically hierarchical index could offer the seamless and logical continuity from genome to human/environment. The EBM based quality assessment enhanced the reliability of knowledge, and the knowledge representation based on the logical conceptual unit approach offered the unification of the different grain size knowledge.