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Hi Richard,
one thing that definitely will slow down almost all operations is if you have large import closures, i.e. a graph that owl:imports many other graphs (transitively). This is because all queries will need to go against the various subgraphs individually and the results then merge (we do not use/have a shared index across all these graphs).
OTOH only some operations will become slower if you have hundreds or thousands of individual graphs that are largely independent. For example the page to browse all Data Graphs will become slower. I am aware of customers that have hundreds of graphs. If you run into significant problems in that area then please let us know.
Holger
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