The Jena Ontology API is language-neutral: the Java class names do not mention the underlying language, e.g: OntClass and ObjectProperty). To represent the differences between the various representations, each of the ontology languages has a profile, which lists the permitted constructs and the URI's of the classes and properties. Thus in the DAML profile, the URI for object property is daml:ObjectProperty, in the OWL profile is it owl:ObjectProperty and in the RDFS profile it is null since RDFS does not define object properties.

The profile is bound to an ontology model, which is an extended version of Jena's Model class. The general Model allows access to the statements in a collection of RDF data. OntModel extends this by adding support for the kinds of objects expected to be in an ontology: classes (in a class hierarchy), properties (in a property hierarchy) and individuals. The properties defined in the ontology language map to accessor methods. For example, an OntClass has a method to list its super-classes, which corresponds to the values of the subClassOf property. This point is worth emphasizing: no information is stored in the OntClass object itself. When the OntClass listSuperClasses() method is called, the information is retrieved from the underlying RDF statements. Similarly adding a subclass to an OntClass asserts an additional RDF statement into the model.

The statements that the ontology Java objects see depend on both the asserted statements in the underlying RDF graph, and the statements that can be inferred by the reasoner being used (if any).