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[bioontology-support] NCIT

Trish Whetzel whetzel at
Mon May 14 12:25:47 PDT 2012

Hi Sina, 

I have not loaded NCIt myself, I only do the pre-processing. I've looped this thread back to the user support mailing list so that either another user who has loaded NCIt can comment and/or one of the developers who loads NCIt into the NCBO BioPortal instance can provide additional help.


On May 14, 2012, at 9:46 AM, Madani,Sina wrote:

> Hi Trish,
> update on NCIT preprocessed load into 0.5 appliance
> - If I use "submit new ontology" form, fill up the meta data for NCIT owl file and use your zip file, the appliance starts processing immediately after load (in contrast to manual start from bioportal admin console in previous version) and throws below error constantly every 5 seconds
> INFO: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'bioportal_protege.tbl_10001' doesn't exist
> - If I use a dummy file during load (instead of the actual zip file you gave me) and then manually upload the original NCIT file into the designated folder and manually start processing in admin console, I get an error complaining that the loaded file name is different from the actual thesaurus owl file and process stops.
> - if I use a dummy (non empty) file with exactly the same name as the NCIT owl file name you sent me and then manually start processing in admin console, processing goes smoothly  through the initial steps (for almost 20 minutes) but finally I get this error . Any hint?   Thanks!
> INFO: 201000/242502, Mon May 14 04:31:52 PDT 2012, delta=8, mem(f/t/m)=770558/2146172/2146172
> May 14, 2012 4:31:53 AM copyKnowledgeBase
> WARNING: Errors at copying knowledgebase jdbc:mysql://localhost/bioportal_protege?useUnicode=true&characterEncoding=UTF-8&holdResultsOpenOverStatementClose=true
> java.sql.SQLException: Can't call commit when autocommit=true

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