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In this paper we describe an infrastructure for query answering over distributed ontologies on the Semantic Web. This infrastructure addresses (i) the coordination of multiple nodes using metadata about the provided resources managed in a decentralized registry and (ii) the mediation between heterogeneous ontologies via an expressive mapping formalism along with corresponding reasoning algorithms for query answering. Our approach is based on a virtual integration that exhibits a semantics as if all ontologies were integrated locally. Practically, the distributed ontologies still reside on the remote peers, and only the parts relevant for answering the query need to be retrieved to the local node. Experimental evaluations with the implementation in KAONp2p show that the approach is very promising, as the performance of query answering is essentially dominated by the size of the data, and only slightly affected by the degree of distribution and heterogeneity.