Database specialized in storing directed graphs?

[flyingfrog]

Don't really know if this will be useful but i'd try pytables:
http://www.pytables.org/moin
it deals very well with every kind of hierarchical data sets, doesn't
matter the size.
It will let you load only significant data, and you'll be able to
query your data.
It's built on top of HDF5 libraries but exposes a very friendly
pythonic interface.
Surely you'll still have to implement all of the graph logic yourself
but this could be a good starting point.
Hope it helps

Marco