I installed Protégé version 4 alpha last night and it has been solid for me so far. It has been over a year since I upgraded my local Protégé installation, and I like these (new ?) features a lot:

• Saved XML for OWL ontologies is very readable, with good automatically generated comments and a nice layout
• Use of the Java OWL API
• Both Fact++ (using JNI) and Pellet 1.5 are smoothly integrated
• The Owlviz Plug-in seems to display graphs faster
• Drag and drop can be used rearrange class hierarchies

I have started working again on an old KnowledgeBooks project: an OWL ontology for news stories and associated "Semantic Scrappers" to populate the ontology from plain texts of news stories. I am still in the experimentation stage for the semantic scrapper: I am trying to decide between pure Ruby code, Java using the available OWL APIs, or a combination of JRuby and the Java OWL APIs. I am currently playing with these three options - for now, I am in no hurry to choose a single option. Using a dynamic language like Ruby has a lot of advantages as far as generating "OWL classes" automatically from an ontology, etc. That said, the Java language has the best semantic web tools and libraries.

Long term, I would like a semi-automatic tool for populating ontologies via custom scrapper libraries. I say "semi-automatic" because it would be useful to integrate with Protégé for manual editing and browsing, while supporting external applications accessing data read-only (?) via the Java OWL APIs.