SNOMED authoring tool

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SNOMED authoring tool

D Piunno
We are new to Protege.  I've searched archives but did not find any posts
pertaining to our question:

Can we use Protege to update SNOMED CT content (add new concepts & synonyms)
for our internal hospital uses?



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Re: SNOMED authoring tool

Michael DeBellis-2
There was some discussion about this a while ago. My recollection (which could be wrong) is that there were some issues with loading SNOMED CT into Protege but someone (not from the Protege team, but from some other company or organization) was working on them. I hope whoever was doing that is reading and will chime in because I'm interested in this question too. 

One thing I can suggest is that you might want to increase the amount of memory that Protege asks Java to allocate for it. I think that ontology is pretty large and there can be issues using the out of the box settings for Protege when dealing with ontologies of that size. I increased my memory for a different project where I had a large (but not that large, thousands of objects) ontology. In your root Protege directory there should be a file called: Protege.l4j.ini  I changed my version of the file so now it looks like this:

-Xms200M
-Xmx2000M
-Xss16M

I think the Xmx setting is the one that gives you more memory and that I added another zero to the default number. 

Michael

On Tue, Sep 24, 2019 at 6:20 AM D Piunno <[hidden email]> wrote:
We are new to Protege.  I've searched archives but did not find any posts
pertaining to our question:

Can we use Protege to update SNOMED CT content (add new concepts & synonyms)
for our internal hospital uses?



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Sent from: http://protege-project.136.n4.nabble.com/Protege-User-f4659818.html
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https://mailman.stanford.edu/mailman/listinfo/protege-user

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Re: SNOMED authoring tool

Campbell, James R
Hi! 
We are loading and working with SNOMED CT International plus Nebraska Lexicon  extension plus US extension plus Australian extension in Protege with OWL.  I agree with your observation but for the 450MB OWL file we load, I use
Xmx 16000M
Xms 4000M
Xmi 320M
and you should make those changes to run.bat in Protege root directory
Jim Campbell
University of Nebraska

From: protege-user <[hidden email]> on behalf of Michael DeBellis <[hidden email]>
Sent: Tuesday, September 24, 2019 8:11 AM
To: User support for WebProtege and Protege Desktop <[hidden email]>
Subject: Re: [protege-user] SNOMED authoring tool
 
Non-UNMC email
There was some discussion about this a while ago. My recollection (which could be wrong) is that there were some issues with loading SNOMED CT into Protege but someone (not from the Protege team, but from some other company or organization) was working on them. I hope whoever was doing that is reading and will chime in because I'm interested in this question too. 

One thing I can suggest is that you might want to increase the amount of memory that Protege asks Java to allocate for it. I think that ontology is pretty large and there can be issues using the out of the box settings for Protege when dealing with ontologies of that size. I increased my memory for a different project where I had a large (but not that large, thousands of objects) ontology. In your root Protege directory there should be a file called: Protege.l4j.ini  I changed my version of the file so now it looks like this:

-Xms200M
-Xmx2000M
-Xss16M

I think the Xmx setting is the one that gives you more memory and that I added another zero to the default number. 

Michael

On Tue, Sep 24, 2019 at 6:20 AM D Piunno <[hidden email]> wrote:
We are new to Protege.  I've searched archives but did not find any posts
pertaining to our question:

Can we use Protege to update SNOMED CT content (add new concepts & synonyms)
for our internal hospital uses?



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