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[bioontology-support] Loading Snomed into the V1.0 appliance

Ray Fergerson ray.fergerson at stanford.edu
Fri May 24 17:38:28 PDT 2013


Marc,

 

Lian should be able to help you get SNOMED loaded into a VM.

 

Ray

 

From: Kohli, Marc David [mailto:mkohli at iu.edu] 
Sent: Friday, May 03, 2013 4:46 PM
To: Ray Fergerson
Cc: <support at bioontology.org>; Lian, Zonghui
Subject: Re: [bioontology-support] Loading Snomed into the V1.0 appliance

 

I've tried to load individual ontologies - including just DSM-IV which is
one of the smallest that I could find from the UMLS metathesaurus. 

 

All I really need to load is SNOMEDCT

 

Thanks,

Marc

 

On May 3, 2013, at 6:19 PM, Ray Fergerson <ray.fergerson at stanford.edu>

 wrote:





Marc,

 

The metathesaurus may be too big to load into a BioPortal VM. You might be
better off loading the individual ontologies that you want.

 

Lian (copied) can help you if you have questions about loaded particular
UMLS ontologies.

 

Ray

 

From: bioontology-support-bounces at lists.stanford.edu
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Kohli, Marc David
Sent: Monday, April 22, 2013 10:48 AM
To: support at bioontology.org
Subject: [bioontology-support] Loading Snomed into the V1.0 appliance

 

All,

Is there anywhere that the procedure for loading an UMLS Metathesaurus RRF
into the bioportal is documented step by step?  I've searched the support
list and found bits and pieces, and tried lots of things.

I have the virtual machine up and running.  I can load RadLex if I
download it via REST from bioportal.bioontology.org so I know that an
appropriately formatted ontology can be loaded into my virtual machine
appropriately.

I've tried to upload both DSM4 in RRF (~140 MB) and SNOMEDCT (~500MB)  I
increased the RAM on the VM to 10 Gb, and I'm not close to being out of
disk space.

I'm happy to post error logs but I'm not sure which log is important
(rails, tomcat, 4store, lexgrid?).

Apologies in advance for the noob questions, and thanks in advance.

Thanks,
Marc

 

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