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RDF is the data interchange layer for the Semantic Web. In order to manage the increasing amount of RDF data, an RDF repository should provide not only the necessary scalability and efficiency, but also sufficient inference capabilities. Though existing RDF repositories have made progress towards these goals, there is still ample space for improving the overall performance. In this paper, we propose a native RDF repository, System II, to pursue a better tradeoff among system scalability, query efficiency, and inference capabilities. System II takes a hypergraph representation for RDF as the data model for its persistent storage, which effectively avoids the costs of data model transformation when accessing RDF data. Based on this native storage scheme, a set of efficient semantic query processing techniques are designed. First, several indices are built to accelerate RDF data access including a value index, a labeling scheme for transitive closure computation, and three triple indices. Second, we propose a hybrid inference strategy under the pD* semantics to support inference for OWL-Lite with a relatively low computational complexity. Finally, we extend the SPARQL algebra to explicitly express inference semantics in logical query plan by defining some new algebra operators. In addition, MD5 hash value of URI and schema level cacheare introduced as practical implementation techniques. The results of performance evaluation on the LUBM benchmark and a real data set show that System II has a better combined metric value than other comparable systems.