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My intuition says that ontology engines like Triplestore or Seseme are going to be slower to query than a DB, but is that really the case? What is it that would make them so much slower?

A: 

Basically, the answer is 'yes'. This is due to the fact that many Ontology engines use an RDBMS data model behind the scenes to manipulate the ontology. But if you happen to find a thorough engine that does not rely on RDBMS, then it needs benchmarking to find out.

Hope this helps! -- etamar.

Etamar L.