Gary's software is available at: http://sig.biostr.washington.edu/share/downloads/OntologyView.zip

To run in Windows, unzip and double-click on the _run.BAT file.

For a Mac (or similar on Linux), open a Terminal and run the following (because it needs Java 1.6):

cd $MY_UNZIP_DIR/OntologyView/Code
JAVA=/System/Library/Frameworks/JavaVM.framework/Versions/1.6/Commands/java 
$JAVA -cp prefuse.jar:lucene-core-2.2.0.jar:. ontologyview/OntologyView

Gary made three interactive embedded tutorials to teach the user about the system; click on Load workspace or tutorials and then scroll down and open one of the tutorial.*.work files.

Gary discusses OntologyView in his PhD dissertation: theory and implementation in Chapter 5 (pages 62-81) and the interface in Chapter 6 (pages 82-125).