I have around 3500 flood control facilities that I would like to represent as a network to determine flow paths (essentially a directed graph). I\'m currently using SqlServer an
Yes (maybe). Your data set sounds relatively small, you could load the graph to memory as an adjacency matrix or adjacency list and query the graph directly - assuming you program.
As far as on-disk format, DOT is fairly portable/popular among others. It also seems pretty common to store a list of edges in a flat file format like:
vertex1 vertex2 {edge_label1}+
Where the first line of the file contains the number of vertices in the graph, and every line after that describes edges. Whether the edges are directed or undirected is up to the implementor. If you want explicit directed edges, then describe them using directed edges like:
vertex1 vertex2
vertex2 vertex1