I've thought about a few resources for you to check out. First, the Manchester Pizza tutorial just rocks when it comes to understanding how to put together an OWL ontology. In particular, it clarifies some of the subtle distinctions between object-oriented modeling, relational models, and description logics, particularly the open-world assumption.
Barry Smith's Relationship ontology is important for thinking about what kinds of relationships to reuse. Note that the OBO ontologies he refers to use DAG-Edit style ontologies, not OWL-style ontologies. DAG-Edit has been typically used more for things like generating large hierarchical classification schemes than it has been used for representing database schemas in a generalizable way. The relationship ontology helps bridge that goal, should you choose to go that route.
However, if you do consider DAG-Edit, as a warning, you should read this critique of MGED and other Bio-ontologies.