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Extract-Transform-Loading (ETL) tools integrate data from source side to target in building data warehouse. However data structure and semantic heterogeneity exits widely in the enterprise information systems. On the purpose of eliminate data heterogeneity so as to construct data warehouse, this paper introduces domain ontology into ETL process of finding the data sources, defining the rules of data transformation, and eliminating the heterogeneity. In this method, the domain ontology is embedded in the metadata of the data warehouse. Hence, the data record could be mapped from data bases to ontology classes of Web Ontology Language (OWL). As result, the accessing of information resources could be done more efficiently. The method is testing in a hospital data warehouse project, and the result shows that ontology method plays an important role in the process of data integration by providing common descriptions of the concepts and relationships of data items, and medical domain ontology in the ETL process is of practical feasibility.