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[protege-dev] [Protege 3.4] Developing a plugin to visualize the FMA. Have a few question

Tania Tudorache tudorache at
Thu Sep 18 15:23:50 PDT 2014

You probably need to increase the heap size for Protege 5. Edit the or run.bat and change the argument -Xmx500M.

I tried it with 4000M, and it loads the FMA owl file in 50 seconds.

You are right, that with the Protege 3 database backend, you would have 
a faster load time, but then all operations that would follow 
(read/writes) would be slower as they happen in the database. Protege 5 
will read the ontology in memory (so you have a longer load time), but 
then all following operations would be very fast as they happen in 
memory. There is always this trade-off.

I suggested to implement a plugin for Protege 4/5 because this is the 
current version. Protege 3 is not under development anymore.

The OWL-API underlying Protege 4/5 is also very well documented and 

Good luck!

On 09/16/2014 04:27 PM, Luchen wrote:
> Hi Tania!
> I've tried using the OWL file in Protegé 5 but performance took a noticeable
> hit when dealing with the FMA this way while Protegé 3.4 ran smoothly.
> Though i have no actual knowledge of how either software actually works i'd
> guess that it has something to do with response time of queing a local
> database instance in the case of protege 3.4 (which one of the steps in the
> setup) vs. loading and parsing the .owl file.
> Is there anyway i can get around this? I'm checking the Protege 5
> documentation as we speak just be ready, but would you personally recommend
> developing this plugin for Protegé 4 or 5?
> --
> View this message in context:
> Sent from the Protege Developer mailing list archive at
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> protege-dev at

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