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With the increase of the number of independent database applications, Large organizations are eager to an effective solution of heterogeneous and distributed databases integration. Ontology is defined as an explicit formal specification of a shared conceptualization. It can provide semantics through relations between concepts and can be widely used on heterogeneous data. This paper mainly discusses two key techniques in ontology-based heterogeneous database integration system: mapping between database schema and creation of global ontology. In our approach, structured, semi-structured, and unstructured data sources are incorporated and provide users and applications with a uniform view. Our initial experiments have shown that the method is able to find the appropriate data often enough to be useful as an exploratory tool, while sheltering users from schema heterogeneity and automatically filling in some incomplete data.