I want to know if there is a java library that can help me show an ontology as a tree in the user interface by taking an OWL file and generating the corresponding tree. I found exactly what I want in OntologyOnline's jOWL but it's for web application; is there something like that for desktop applications?
See the OWL API at https://github.com/owlcs/owlapi. The API provides a means to load the Ontology from files or UIs and a Visitor to walk the ontology. You can use the visitor to to build your own tree for display purposes - a Swing JTree for example.