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In this paper, we present a novel approach for the management of the ontology-based knowledge management system. It extends our previous work in the ontology evolution by taking into account the usage of the ontology in the knowledge management system. The approach is mainly based on the analysis of the users' behaviour in two phases of a knowledge management cycle: (i) in providing knowledge by analysing the quality of annotations and (ii) in searching for knowledge by analysing users' queries and the responses from the knowledge repository. This analysis results in the recommendations for changes in the underlying ontology, the annotations and/or the knowledge repository in order to make the whole system more efficient. We present two short case studies.