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[bioontology-support] help loading rxnorm to ncbo virtual appliance

Trish Whetzel whetzel at stanford.edu
Thu Jan 17 15:29:08 PST 2013


Hi Greg, 

Have you been able to sort out the Annotator population issue or get feedback from other users of the virtual appliance? 

Trish 


On Sep 18, 2012, at 7:22 AM, Gardner, Gregory Allen wrote:

> Hi,
> 
> Sorry for the delay in an update.  We were able to successfully load RxNORM in the virtual appliance.  Disk space was the issue, I increased the virtual disk size to 25Gb and the ontology parsed just fine (about 10Gb of total space was used after the ontology was loaded). 
> 
> However, I'm now trying to setup the Annotator Dataset Workflow using the instructions at http://www.bioontology.org/wiki/index.php/Annotator_Dataset_Workflow_Howto  
> 
> When executing the populate concepts step, the software seems to continue to run as long as we allow it to.  I have tried this twice, the first time it ran for about a week before I stopped it.  I then ran the sql commands to clean up the database (#1 under the Data Clean-Up section of the wiki), although I had to add a sql command to remove data from another table that has foreign key references to the obs_concept table.  I then ran the concept loader again, but stopped it after a day.  Both times the status in the obs_ontology table moved from 11 to 12, then stayed at 12 indefinitely.  No errors were reported in the tomcat log or the obs_error_queue table.  Any ideas what might be going on?
> 
> Thanks,
> Greg
> 
> -----Original Message-----
> From: Lian, Zonghui [mailto:Lian.Zonghui at mayo.edu] 
> Sent: Thursday, August 09, 2012 4:03 PM
> To: Paul R Alexander; Gardner, Gregory Allen
> Cc: Boyce, Richard David; support at bioontology.org; Stancl, Craig R.
> Subject: RE: [bioontology-support] help loading rxnorm to ncbo virtual appliance
> 
> Hi Greg,
> 
> Do you have update for this issue?
> 
> I tested it by loading the same ontology on my desktop with the lexbig GUI (the bioportal's back end loader is based on it). It is no problem. The config for my appplication is:
> Xmx1000M -XX:MaxPermSize=256M
> 
> Bioportal may take more memory since it is bigger than lexbig. I guess the change you made in tomcat6.conf (5GB or 6GB) should OK. 
> 
> The error message "LexBIG ontology failed to load, exitcode=NON-RECOVERABLE" mean the previous failed loaded ontology's registration is still there. Can you take a try -- remove it with admin tool. If it does not work. You may need to install a lexbig GUI, which can help you to fully clean the registration. 
> 
> Thanks,
> Lian
> 
> 
> 
> -----Original Message-----
> From: Paul R Alexander [mailto:palexander at stanford.edu]
> Sent: Tuesday, August 07, 2012 8:53 PM
> To: Gardner, Gregory Allen
> Cc: Boyce, Richard David; support at bioontology.org; Lian, Zonghui
> Subject: Re: [bioontology-support] help loading rxnorm to ncbo virtual appliance
> 
> Greg,
> 
> I'm looping Lian in to this conversation to see if he has any insight (Pradip has moved on to another project, so Lian is the contact at Mayo now). One of the things I can think to check is disk space. Is it possible that it's filling up the space you have available on the Appliance?
> 
> Lian -- any other ideas?
> 
> Paul
> 
> 
> On Tue Aug  7 04:52:04 2012, Gardner, Gregory Allen wrote:
>> Please help -- after many different attempts to load RXNORM into the NCBO virtual appliance, we are at a dead end (see below for errors and setup).  Do you know what might be going wrong, or do you have a virtual appliance with RxNORM pre-loaded?
>> 
>> Our initial error on attempting to load the RxNorm ontology (downloaded from http://rest.bioontology.org/bioportal/ontologies/download/46395) was a Java NullPointerException on the parse ontologies screen of the bioportal admin.
>> 
>> We're running the appliance on version 11.10 of Ubuntu in VirtualBox.  Due to our local network, we set the appliance to run with a host-only network adapter, rather than the default bridged adapter.
>> Since the vm ip is then assigned by VirtualBox and cannot connect to an external network, we modified the rails bioportal configuration, setting the local_ip variable to the static ip assigned by virtualbox.
>> Initially, we tried running with 4 gb of ram, increasing to 6.5 gb (the maximum our system can handle) after the initial failure.  When running the vm at 6.5 gb of ram, we configure tomcat to use up to 5gb of ram by editting /etc/tomcat6/tomcat6.conf, changing the java opts from -Xmx2G to -Xmx5G.
>> 
>> We load the local copy of rxnorm according to the instructions given to us by Pradip.  Initially, a zip file with a dummy RRF file is loaded through the new ontology screen of bioportal (../ontologies/new).  The folder where the appliance is placing the ontology files is then determined, and the local rxnorm RRF files are copied to this directory.
>> The status of the ontology in the appliance at this point is "1", 
>> waiting to parse.  We then tell bioportal to parse the new ontology at 
>> the bioportal admin parse ontologies screen.  After clicking run, the 
>> ontology status changes to "2", parsing.  Bioportal continues to parse 
>> the ontology for ~1-2 hours, at which point the above error is seen.
>> Running at
>> 4 gb of ram, the virtual machine also printed an "out of memory" error.  At 6.5 gb, the process did not complete and eventually caused the host system to lock.  Perhaps we do not have the memory required to load rxnorm ourselves?
>> 
>> During various attempts to load the ontology, I occasionally also saw an error to the effect of "LexBIG ontology failed to load, exitcode=NON-RECOVERABLE" soon after (~10-20 seconds) telling the appliance to parse the new ontology.  This seemed to occur when a previous attempt at loading RxNorm had failed and I tried to load it again under a different name without reloading a fresh copy of the appliance into VirtualBox.
>> 
>> Please let me know if I can provide any further information.
>> 
>> Thank you for your help,
>> 
>> Greg Gardner
>> Software Developer
>> Department of Biomedical Informatics
>> University of Pittsburgh
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