Efficient Mutable Graph Representation in Prolog?

As usual: Using the dynamic database gives you indexing, which may speed things up (on look-up) and slow you down (on asserting). In general, the dynamic database is not so good when you assert more often than you look up. The main drawback though is that it also significantly complicates testing and debugging, because you cannot test your predicates in isolation, and need to keep the current implicit state of the database in mind. Lists of nodes and adjacancy connections are a good representation in many cases. A different representation I like a lot, especially if you need to store further attributes for nodes and edges, is to use one variable for each node, and use variable attribtues (get_attr/3 and put_attr/3 in SWI-Prolog) to store edges on them, for example [edge_to(E1,N_1),edge_to(E2,N_2),...] where N_i are the variables representing other nodes (with their own attributes), and E_j are also variables onto which you can attach further attributes to store additional information (weight, capacity etc.) about each edge if needed.