Metaphysical Ontology

When creating an object-oriented analysis of anything, perhaps a business problem, do you assume that the categorical hierarchy you develop reflects the “true nature” of the phenomena you are analyzing?  Do you assume a metaphysical ontology?

http://en.wikipedia.org/wiki/Ontology

How does ontological categorization differ from category theory in mathematics?

http://en.wikipedia.org/wiki/Category_theory

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