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From "Tsung-Ting Kuo" <ts...@ucsd.edu>
Subject RE: Question about YTEX
Date Wed, 10 Jun 2015 21:32:11 GMT
Thanks very much, this is really helpful! I surely can see the “v_snomed_fword_lookup”
table in my database!

 

So my next question is: would there be any document to tell me how to setup the Clinical NLP
Semantic Search Engine on Tomcat (actually this is the main purpose why I am seeking for YTEX’s
help)? I saw “ctakes-ytex-web-3.2.2-classes.jar” in the “lib” folder, but I am not
sure how to deploy it as a web service.

 

Best regards,

Tim

 

 

From: Vijay Garla [mailto:vijay.garla@yale.edu] 
Sent: Wednesday, June 10, 2015 12:10 PM
To: tskuo@ucsd.edu
Cc: Vijay Garla; dev@ctakes.apache.org
Subject: Re: Question about YTEX

 

You should see a v_snomed_fword_lookup table in your database.

 

YTEX doesn't use all UMLS.  It filters to SNOMED-CT and RXNORM, and specific Semantic Types

 

The script is uses is here: https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-ytex/scripts/data/mysql/umls/insert_view.template.sql

 

You can create a dictionary with different vocabularies/semantic types very easily (just change
the sql slightly).  

 

For more detail on how this works, see https://code.google.com/p/ytex/wiki/DictionaryLookup_V07
(docs slightly out of date).

 

I have not tested this with the 'fast' dictionary lookup, but I think the main speed gain
of the fast lookup is due to skipping an extra(neous) database query.

 

HTH,

 

VJ

 

On Wed, Jun 10, 2015 at 8:15 PM, Tsung-Ting Kuo <tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>
> wrote:

BTW, my YTEX installation just completed, and the results is attached. Does my YTEX installation
create dictionary lookup table with all concepts from the UMLS successfully?

 

Thanks very much!

 

Best regards,

Tim

 

From: Tsung-Ting Kuo [mailto:tskuo@ucsd.edu <mailto:tskuo@ucsd.edu> ] 
Sent: Wednesday, June 10, 2015 9:49 AM
To: 'Vijay Garla'; dev@ctakes.apache.org <mailto:dev@ctakes.apache.org> 
Subject: RE: Question about YTEX

 

Hi Vijay,

 

You are absolutely right – after changing the permission of the “resource” directory,
YTEX start installing without problem! In the meanwhile, I have a quick question: since I
have installed the UMLS database and set the “umls.schema” to UMLS database name (I am
using MySQL), how do I know whether YTEX successfully creates a dictionary lookup table with
all concepts from the UMLS or not?

 

Thanks again!

 

Best regards,

Tim

 

From: Vijay Garla [mailto:vijay.garla@yale.edu] 
Sent: Tuesday, June 9, 2015 11:31 PM
To: tskuo@ucsd.edu <mailto:tskuo@ucsd.edu> ; dev@ctakes.apache.org <mailto:dev@ctakes.apache.org>

Cc: vijay.garla@yale.edu <mailto:vijay.garla@yale.edu> 
Subject: Re: Question about YTEX

 

Hi Tsung-Ting,

 

I see the following error:

 

templateToConfig.extractTemplates:

     [echo] unpacking ytex templates from /usr/local/apache-ctakes-3.2.2/lib/ctakes-ytex-res-3.2.2.jar
to /usr/local/apache-ctakes-3.2.2/resources

    [unzip] Expanding: /usr/local/apache-ctakes-3.2.2/lib/ctakes-ytex-res-3.2.2.jar into /usr/local/apache-ctakes-3.2.2/resources

    [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGraph/sct-rxnorm.template.xml

    [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGraph/sct-msh-csp-aod.template.xml

    [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/conceptGraph/sct-umls.template.xml

    [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/umls/model/UMLS.hbm.template.xml

    [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_stem_SNOMED.template.xml

    [unzip] Unable to expand to file /usr/local/apache-ctakes-3.2.2/resources/org/apache/ctakes/ytex/dictionary/lookup/LookupDesc_SNOMED.template.xml

 

I don't know why there was an issue extracting ctakes-ytex-res-3.2.2.jar.  Can you make sure
that  /usr/local/apache-ctakes-3.2.2/resources exists and is writable?

 

-vj

 

On Wed, Jun 10, 2015 at 12:17 AM, Tsung-Ting Kuo <tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>
> wrote:

Hi Vijay Garla,

 

I am Tsung-Ting Kuo from UCSD, and I am interested in your YTEX project. I tried to download
it and setup based on the following page:

 

https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation <https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_confluence_display_CTAKES_YTEX-2BInstallation&d=AwMFAg&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=rw3vAb56jh8xMYlMHfE0hS2hfbV3RFxqvusA5jfoLnc&m=b0QIg7D5IImLEUt69gE-sqJU5GHeSBEMS_oz2Uddul4&s=Jyu357olHH-y9kNgTHIj2B01-i6DhsiGYH2HOwu9yok&e=>


 

However, in the final step (step 7), I was not able to setup. The attached “setup.out”
seems to show that the “UMLS.hbm.xml” is missing. Could you kindly help to tell me how
to set it up?

 

Thanks very much!

 

Best regards,

Tsung-Ting

 

 

 


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