All people in computer science and some fields of engineering (e.g. industrial engineering?) are very familiar with “Graphs” — those nodes and arcs. And, actually, we can represent the web as a [huge] graph. Where node=webpage, arc=(hyper)link.
From this representation, it gives us a way to understand the characteristic of the web better (as we do well with normal graphs).
Talking about representing document/site as a node in a graph, Peer-to-Peer people already done this since their early day.