We present the GeneTegra system, an ontology-based information integration environment. We show its ability to query multiple data sources, and we evaluate the relative performance of different data repositories. GeneTegra uses Semantic Web standards to resolve the semantic and syntactic diversity of the large and increasingly complex body of publicly available data. GeneTegra contains mechanisms to create ontology models of data sources using the OWL 2 Web Ontology Language, and to define, plan, and execute queries against these models using the SPARQL query language. Data source formats supported include relational databases and XML and RDF data sources. Experimental results have been obtained to show that GeneTegra obtains equivalent results from different data repositories containing the same data, illustrating the ability of the methods proposed in querying heterogeneous sources using the same modeling paradigm.