small update:

The issue from the previous post was one of indexing. The Property object identifiers were being generated differently for every Neuron object which obviously made minimal use of the index. Basing identifiers on the identity of the owner object and the value of the property takes the query time to get a single property back to constant time. For example:

for x in range(1000):
    Neuron().save() # creates and saves a randomly generated neuron object
Neuron().name()

Takes about 10 seconds for the call to name() on rdflib's memory store as well as the SleepyCat store (closer to 11 seconds) bundled with rdflib. That's about .01 seconds for getting the name of a specific neuron regardless of the database size.