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In this paper we present the conceptual architecture of ONTOLOGER, a system for usage-driven management of querying for information in ontology-based information portals. The system is based on the analysis of users' activities that are acquired in the so-called semantic log file, which contains information about the content of a visited page as well. These analyses are used for managing (i) the underlying ontology, (ii) querying mechanism and (iii) the content of the information repository, in order to ensure that (a) the structure of the vocabulary reflects the needs of users, (b) the highly-relevant results can be found by users although they make short queries and read only top-ranked results and (c) the information repository contains (only) resources users are interested in. The focus of the paper is on improving querying (retrieval) mechanism based on the usage data. We present a case study, which shows how a portal can benefit from implementing presented management system.