Provided is a data processing method for clinical decision support system. The data processing method provides an algorithm capable of performing parsing based on an Ontology technique and automatically updating rule database in order to reduce time and labor overloads accompanied by update of the rule database. According to an aspect, the data processing method includes inferring input data having a natural language format based on an Ontology technique to recognize at least one input rule included in the input data; inferring storage data having a natural language format and stored in rule database based on the Ontology technique to recognize at least one storage rule associated with the input rule from the storage data; comparing the input rule to the storage rule using a Self Evolutionary Rule-base algorithm; and updating the storage data stored in the rule database to the input data according to the result of the comparison.