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[bioontology-support] 0.5 appliance loading error for SNOMED

Trish Whetzel whetzel at
Tue May 1 17:19:24 PDT 2012

Hi Pradip, 

Is this item from the user support mailing list one that you can help Sina with?


On Apr 30, 2012, at 8:28 AM, Madani,Sina wrote:

> Hi ,
> Loading SNOMED into Bioportal V 0.5 went through until the end of indexing. But at the very last step I got below error and parsing failed (lexevs log file attached). Do you have any suggestion to fix this? I tried this twice and both times it failed at the very same step.
> com.mysql.jdbc.exceptions.jdbc4.CommunicationsException: Communications link failure
> Googling the error points to the issue of "netTimeoutForStreamingResults" for very large datasets...
> Also, I am not sure if this is a related issue or not but I am getting the error shown in the screenshot below whenever I restart ncbo service.
> Is any of the MySQL parameters have been changed in the 0.5 appliance?
> <image001.png>
> Thanks!
> Sina
> <LexBIG_load_log.txt>_______________________________________________
> bioontology-support mailing list
> bioontology-support at

Trish Whetzel, PhD
Outreach Coordinator
The National Center for Biomedical Ontology
Ph: 650-721-2378

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