If you really do require OWL as target language and D2RQ does not cover your needs, you might also want to try the DataMaster and OntoBase Protege plugins. DataMaster lets you choose whether to import just the structure of the database or its data as well and also provides a few modeling alternatives for creating the output ontology. It is also possible that OntoBase offers the option of not importing the data, but I am not sure. Either way, as they are both Protege plugins, it must be fairly easy to do an .owl file export.