Complex DBs & Ontologies

Hello,

I tried to translate a small database schema to an ontology model (following some mapping rules).
However I guess the process would be more complex to do with a big and more constrained relational database.
My question is not specific to Postgresql, But I thought more people in this list are expert about databases :)
So, my question, what are the main problems of big relational databases that will be hard to map into another things (cause in my case "to ontologies" I don't want to lose useful information & constraints ..and so on.. ).

Regards,
Yitaru