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[protege-discussion] DB Backend: Slowdown for classes with thousands of instances

Daniel Holbert holbert at helix.stanford.edu
Mon Oct 30 14:54:28 PST 2006


I'm running Protege using a database backend, and I get a huge slowdown whenever I try to work 
with a class that has more than a few thousand instances.  Has anyone else experienced this, 
and do you have any suggestions for dealing with it?

I have one class that has 5,000 instances and another class that has 23,000 instances.  When 
I'm in the "Instances" tab and I click on the names of these classes, the whole Protege 
program hangs for 15 seconds to load the 5000-instance class and about a minute to load the 
23000-instance class.

I've tried using both a local and a networked DB, and the slowdown remains, so network latency 
is not the bottleneck.  I've also tried using Oracle, MySQL, and postgresql for the DB 
backend, and I haven't found a noticeable difference in speed.

Also, if I convert this project to a standard Protege project (without a DB backend), then it 
runs fairly quickly.  I've only experienced the major slowdown when using a DB backend.

Thanks!
Daniel Holbert
PharmGKB, http://www.pharmgkb.org
Stanford University



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