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Could you explain the issue in a little more detail? I assume you are referring to the model document which is work in progress?
The separation of nomenclature and taxonomy is clear and done. What is your distinction between conceptual and taxonomy? Is it the hierarchical context vs the included content as Rich said in #6?
Things like "geological period" and "synonym" don't belong together at the same level, for example.
@dimus has a nice three tiered model that he defines as a way to organize data. I think things need to be crystal clear there.
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