Nowadays big volumes of medical data are accumulated. So the problem of analysis of these data and mining linked logical structures, defining internal data semantics is an actual one. Solution of this problem allows solve the problem of optimizing intelligent context search. In the article an approach for solving this problem for analyzing processes running in human organism is discussed. Suggested approach is based on building of linked logical structures and assumes finding of motifs in variations of parameters of systems and subsystems. An algorithm of finding of motifs is suggested. The result of algorithm operation is logical structure that reflects internal dependencies which exist in human organism. Nowadays suggested approach is used in Almazov Cardio-logical Center for medical data processing.