I would definitely check out Datomic. The free edition uses H2 internally to persist to disk, it's not just a memory db. The datalog query language for Datomic is great, and you should definitely give it some thoughts. A good overview video on Datomic which I recommend is listed on their site: *Datomic, and How We Built It<http://at.pscdn.net/008/00102/videoplatform/kv/121105techconf_close.html> .* If you think a graph database might be suitable for your case, you may want to check out this comparison page: http://architects.dzone.com/articles/16-graph-databases-compared. OrientDB (http://www.orientdb.org/) might be a suitable lightweight and mature option. It can be embedded and includes various query options: Traverser API, Blueprints, Rexster, Gremlin, and its own SQL-like Query Language. In the case of a graph database t the blueprints API may give you some added benefits as explained here: http://cloud.dzone.com/articles/get-started-tinkerpop. Datomic can also be accessed through the Blueprints API.
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