I'm looking for a graphical browser for examining large networks of OWL/RDF instances. Protege's instance browser isn't really useful and if COE supports instance browsing, I've not discovered how. Network size is around a million nodes.
I'm hoping to be able to search for an instance, expand it to show its relationships, and explore other instances from there. Graphical would be nice, but a plain Jtree would do too.
The Tabulator project from the W3C is designed for browsing RDF data sets. It provides an add-in for Firefox, that may facilitate your explorations. it also has features to make your data browsable remotely using AJAX.
The MIT Simile project developed a faceted browser for RDF called Longwell. This was a research project. Development has now languished, and their demos seem to be broken; however, I can attest to the fact that it works. I use it regularly to browse an extremely miscellaneous collection of RDF instance data on my local machine.
Longwell is written as a Java web application. It comes with its own jetty server or can be run as a servelet. It can be run in memory, or with a variety of back-ends. It parses both rdf/xml and n3, and is highly configurable via velocity templates, css, and the 'Fresnel' RDF display ontology. It's a pity it hasn't been pursued further; I've found its ui to be very agreeable, and particularly useful is the fact that it will browse any RDF instance data you like, with or without schemas or ontologies.