structOntology is the ontology manager application within the conStruct open source semantic technology suite. structOntology is based on the OWLAPI. It also has two other notable advantages (among many): 1) its superior search function (if you have been using Protégé or similar, there is much improvement due to Solr); and 2) its available functionality directly within the applications that use ontologies.

There is a YouTube video link providing a view of the application in action.