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Due to the interconnected, non-simple structure of ontologies, it’s difficult to give a simple diagram that fully models one. Instead, I’m just going to list the broad categories of classes that you find in an application and simply discuss how they actually interconnect.

(via Cocoa with Love: The design of every Mac application )

See also, for a more practical view:

• What are the Xcode solution organisation best practices and guidelines?
• Code Organization in Xcode Projects