How we organize the parts of a system into a whole matters. Every whole has parts. Every part is a whole which has parts. And, every whole is a part of a larger whole. The way we group things is a function of our perspective and the parts we identify a function of distinctions making. Relationships are part of the whole, too, which makes them parts of the whole.
Also see The Dark Side of Categorical Thinking to learn more about Systems, part-whole.