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valimaggi, Welcome to the XOOPS forum!
I'm affraid there is not much documentation about these things. XOOPS is like an organic growth out of PHPNuke and has been extended during almost 10 years by several developers. The various alterations in the database, were done mostly out of practical need and not so much out of conceptual or relational thinking. And if they where, these concepts were not so much discussed, nor documented.
I think the only thing lerft is reverse engineering: following the queries. All sources are available and included in the downloads. For the core, most relations have to do with modules and user(group)s for dealing with preferences and permissions.
There are also some people trying to discover the
design patterns beyond XOOPS. Anyway, we look forward to read the results of your research.