As an example, below is a figure drawn by Kamil Sarac for a paper on multicast monitoring tools. Notice how the figure conveys lots of different information by using axes, lines, and proximity.
The key to this assignment is to be able to describe the sets of acronyms that do have relationships to each other but not to over do it and create relationships where none exist. A good way to start is to use the reference model to layer functionality and then group protocols according to it. The goal is for you to demonstrate that you understand these acronyms beyond just knowing the acronym expansion.
You only need to turn in a hard copy of your homework (due in class), but the assignment must be done entirely in some kind of digital format. Since I will not see the source, you can use anything you want, for example: HTML, Latex, Word, etc.