Semantic data management is a key issue in integration of heterogeneous biological data. Traditional database system is not suitable for complex semantic datamanagement.Moreover, most of the biological data management systems cannot provide efficient semantic search over database. In this paper, we present a data warehouse which adopts the object deputy model to store semantic biological data. Most important of all, we can provide more convenient and efficient semantic search for users. The experiment results show that our approach ismore feasible and efficient than the traditional one.