I can't speak to the duplicates issue, though I know it's common in 
logic-based solutions.  In specific cases, I suspect the problem could be 
solved (or ameliorated) by tabling but I'm just getting into logic 
programming so I'm not too sure about that.

Overall, your use case sounds very similar to mine.  I've thought that the 
marriage of an inference engine and a graph database would yield a very 
powerful tool.  I'm looking forward to an abstraction layer that lets me 
bind any data store and, even more powerfully, multiple data stores to the 
logic engine.

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