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[bioontology-support] FW: Need some assistance

Trish Whetzel whetzel at
Sun Jul 17 21:35:26 PDT 2011

Hi Lori,

I'm away at a conference. In order to get the ontology abbreviation or SAB, you can use the "List latest versions of all ontologies" [1] Web service, the ontology abbreviation is in the element <abbreviation>. Therefore, this information can be accessed directly in your i2b2-NBCO extraction tool.  

The wiki page you refer to was generated when we first starting working with i2b2 a few years back. The files contain the ontology abbreviations and the initial i2b2 formatted data based on the first version of the script we developed to provide ontology data in the i2b2 format used at that time. Our infrastructure has changed since this initial work was done (and the i2b2 format), hence the need for the new i2b2-NCBO code. 



On Jul 14, 2011, at 7:55 PM, Phillips, Lori C. wrote:

> Forwarding this message (Trish is on vacation)
> From: Phillips, Lori C. 
> Sent: Thursday, July 14, 2011 1:55 PM
> To: 'Trish Whetzel'
> Subject: Need some assistance
> Hi Trish,
> I have seen a reference to SABs on the Path to Root page
> "-ontologies : The complete path of the file containing the SABs of the ontologies to be used. The file should contain one SAB 
>                  on every line. Please see SABsTest.txt and SABsComplete for the correct format. The path should be of the type 
>                  C:\\Bioportal\\SAB\\SABsTest.txt "
> Can you tell me what kind of info is contained in the file and whether or not this info is a(n) (accepted) standard?
> I am asking not so I can use this path-to-root feature but rather, if its what I think it is (acronyms for ontologies),
> that I need it for my i2b2-NCBO extraction tool.
> Also could you send me the two files:  SABsTest.txt and SABsComplete?  or explain if this info is available via the rest services?
> Thanks for your help
> Lori
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