Supporting semantic queries in relational databases is essential to many advanced applications. Recently, with the increasing use of ontology in various applications, the need for querying relational data together with its related ontology has become more urgent. In this paper, we identify and discuss the problem of querying relational data with its ontologies. Two fundamental challenges make the problem interesting. First, it is extremely difficult to express queries against graph structured ontology in the relational query language SQL, and second, in many cases where data and its related ontology are complicated, queries are usually not precise, that is, users often have only a vague notion, rather than a clear understanding and definition, of what they query for. We outline a query-by-example approach that enables us to support semantic queries in relational databases with ease. Instead of endeavoring to incorporate ontology into relational form and create new language construct...