[whpalmer4]

Do you see yourself using OmniGraffle as the creation tool, and your code extracting information for further processing? How about having your code be the creation tool, and emit an OmniGraffle document? DOT/GraphViz format might be your friend here. I know that Omni uses it for visualizing OmniFocus sync graphs, for example.

Instead of figuring out how to parse the XML, another route would be to write an Applescript for OmniGraffle which communicates with your program in a convenient fashion.