This paper describes an approach to build a Data Definition Ontology (DDO) in the context of full domain ontology integration with datasets in order to share and query clinical heterogeneous data repositories. We have adapted an existing semantic web tool (D2RQ) to implement a process that automatically generates the DDO from a database information model, thanks to reverse engineering and schema mapping approaches. This study has been performed in the context of the DebugIT European project (Detecting and Eliminating Bacteria UsinG Information Technology) that aims to control and monitor the bacterial growth via a semantic interoperability platform (IP). The evaluation of the process is based, first, on the accuracy of the produced DDO for different samples of database storage and second, by checking the congruency between the DDO and the D2RQ database mapping file.