ModelFactory – Inference Model
ModelFactory is the on stop shop for creating Model’s in Apache Jena. ModelFactory is also the way to create Inference models, which offer different kinds of inference over RDF-based models (used for RDFS and OWL) – through reasoners.
One interesting example can be seen here on stackoverflow.
Which does lead back to section 2 and the OpenTox article. Its a shame the article doesn’t go further to show effectively a SPARQL made against a D2RQ data source, but prior to the D2RQ data source being queried, a Reasoner is leveraged to effectively enhance the SPARQL.
Finally, probably worth having a look at these samples around Family Tree.
Tales from a Trading Desk 