Large ontology projects, such as the NCI Vocabulary, are very time-consuming to load into Protégé. The best approach is to build a project from the raw OWL file, and then save it as a Database OWL project.

1. Obtain your OWL file, such as the NCI terminology.
2. Using Protege 2.1 beta (build 199+) and the latest OWL plugin, as well as the appropriate JDBC driver (specified on the classpath) select Build Project ... in the File menu (or the first dialog box). Select the OWL file you wish to load. Protege will now parse the OWL file and load it into memory.
3. Once this process is complete, (the longest part), you should have an ontology to play with in the OWL tab. Now you want to select "Save in Format", and select "OWL Database".
4. This will bring up a screen with the database options. Fill this out according to the instructions for database backends.
5. Protege now saves the project to the database, creating the table if necessary, and then reloads the project from that database format. You can now safely exit Protege ifnecessary. Next time you start Protege, it will load this project from the database much quicker than from flat files.