For right now, we are still unsure of whether to uses these particular graphs or some other formatting, so I am putting of the official documentation until we get a definitive answer.

Here is the short version of how to use these objects:

*AM* => An adjacency matrix 
*BP* => Bait/Prey model
*CM* => Co-membership 
*G*  => Graph (as graphNEL)
ppi* => Protein-Protein Interaction

* implies anything before or after. 