I am the creator of Redland , which includes its own thrice stores in C plus. I used some of Java such as Jena and Sesame.
It's hard to say more without knowing what the problem is, but in general, native triple stores work better if your problematic space / request template is more “graphic” rather than “objective”. An object means that you tend to always manipulate - set / receive the same sample of data each time - in this case you can use ORM or another object-relational mapping and a fixed schema. If your problem and scheme is more dynamic - "Graphy" - you can take a triple approach to storage, where it’s easier to jump over the data than usual in the aka join world.
Of course, there is also an approach to the document, such as CouchDB, but which is difficult to learn from the information you provided.
dajobe
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