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[bioontology-support] NCIT

Madani,Sina AHMadani at
Wed May 9 18:42:08 PDT 2012

Hi Trish,
I am using version 0.5 -
I downloaded the file from your website, the latest version. If that file is not pre-processed, is there any location that I can download it? Tania, previously, pointed me to a location (perhaps wiki) for a preprocessed one (maybe an older version). Should I look in that location again?


From: Trish Whetzel [mailto:whetzel at]
Sent: Wednesday, May 09, 2012 8:39 PM
To: Madani,Sina
Cc: support at
Subject: Re: [bioontology-support] NCIT

Hi Sina,

What version of the VM are you using? Also, did you pre-process NCIt to remove the XML attributes within the property values? This will be useful if you plan to populate the Annotator database with NCIt content since without the pre-processing the synonym values will include additional XML tags and therefore not provide any matches.


On May 9, 2012, at 2:01 PM, Madani,Sina wrote:

I am trying to load NCIT terminology (11.06 downloaded from Bioportal) into our local Bioportal instance v0.5 and getting these errors. Any hint?
I wasn't successful to load SNOMED 2011AB into V0.5 either due to some other MySQL error.


INFO: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'bioportal_protege.tbl_10002' doesn't exist

INFO: com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'bioportal_protege.tbl_10001' doesn't exist
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