  We have compared the performance of five non-commercial triple stores,
Virtuoso-open source, Jena SDB, Jena TDB, SWIFT-OWLIM and 4Store. We examined
three performance aspects: the query execution time, scalability and run-to-run
reproducibility. The queries we chose addressed different ontological or
biological topics, and we obtained evidence that individual store performance
was quite query specific. We identified three groups of queries displaying
similar behavior across the different stores: 1) relatively short response
time, 2) moderate response time and 3) relatively long response time. OWLIM
proved to be a winner in the first group, 4Store in the second and Virtuoso in
the third. Our benchmarking showed Virtuoso to be a very balanced performer -
its response time was better than average for all the 24 queries; it showed a
very good scalability and a reasonable run-to-run reproducibility.
