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

Congmin min marlonmin at
Mon Oct 30 18:46:59 PST 2006

yes, that's really a problem. If the number of instances become bigger, it
can not even be loaded successfully, even though the size of the file may
only be about 40-50 MB. I had similar experiences.

On 10/30/06, Daniel Holbert <holbert at> wrote:
> 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,
> Stanford University
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