We are researching the interaction between the rule and the ontology layers of the Semantic Web, by comparing two options: 1) using OWL and its rule extension SWRL to develop an integrated ontology/rule language, and 2) layering rules on top of an ontology with RuleML and OWL. Toward this end, we are developing the SWORIER system, which enables efficient automated reasoning on ontologies and rules, by translating all of them into Prolog and adding a set of general rules that properly capture the semantics of OWL. We have also enabled the user to make dynamic changes on the fly, at run time. This work addresses several of the concerns expressed in previous work, such as negation, complementary classes, disjunctive heads, and cardinality, and it discusses alternative approaches for dealing with inconsistencies in the knowledge base. In addition, for efficiency, we implemented techniques called extensionalization, avoiding reanalysis, and code minimization.