The ontology technology is developing into a foundation for many of new technologies recently. But the low performance to query or reason over large knowledge bases limits its application in practical fields. Ontology Databases attempt to solve this problem by storing ontology in database tables and facilitating DBMS with rule-based ontology querying and reasoning ability. In this paper, we?ll discuss the features of ontology databases, the progress our work has made in this technology, the syntax of Ont-QL, the representation of ontology and UDR in relational databases, and the algorithm to perform rule-based query and judge. We will also present two examples to illustrate the application of ontology databases, and conclude our discussion by addressing its application perspective at last.