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In this paper, we apply semantic web-based technologies to integrate heterogeneous data from medical information system, and design a heterogeneous data integration model, which combines Mediator/Wrapper framework with ontology, using OGSA-DAI as data accessing middleware. Mediator provides uniform query interface, decomposes user queries based on the mapping relations between global ontology and local ontologies. Wrapper receives subqueries and returns query results to Mediator. To tackle the problem of semantic interoperability, the model uses two-layer ontologies and three-hierarchy mappings, that is the mapping between global ontology and local ontologies, among local ontologies, and the mapping between local ontologies and databases. According to our integration model, users can get query results from heterogeneous medical data sources but need not to know anything about the data sources with heterogeneous semantics.