We study a logic-based approach to versioning of ontologies. Under this view, ontologies provide answers to queries about some vocabulary of interest. The difference between two versions of an ontology is given by the set of queries that receive different answers. We investigate this approach for terminologies given in the description logic EL extended with role inclusions and domain and range restrictions for three distinct types of queries: subsumption, instance, and conjunctive queries. In all three cases, we present polynomialtime algorithms that decide whether two terminologies give the same answers to queries over a given vocabulary and compute a succinct representation of the difference if it is nonempty. We present an implementation, CEX2, of the developed algorithms for subsumption and instance queries and apply it to distinct versions of Snomed CT and the NCI ontology.