Researching visualization software. What we will need for viewing object graphs and tree-structured data. Looks like there are some open source projects that ride on top of Java 2D, and provide visualization features such as layers, zooming, and panning. There are some open source apps built on top of the framework, so customizing may be straightforward.
This chemical model visualizer: http://sali.rguha.net/ depends on the object graph visualizer: http://www.graphviz.org/ which rides on this open source ZVTM project: http://zvtm.sourceforge.net/
The idea would be to have 2D, layered, multi-zoom interface into the trees of the tagonomy, so that tagonomies become visually recognizable and explorable spaces.