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From "Tsung-Ting Kuo" <ts...@ucsd.edu>
Subject RE: Question about YTEX
Date Fri, 12 Jun 2015 17:32:04 GMT
Hi Vijay,

 

I just tried to walk through the fracture demo you mentioned. However, I have two questions:

 

(1)   In the step “3. Configure Analysis Engine”, I could not find places in CPE to assign
“analysis_batch” (I am using cTAKES 3.2.2). Where could I set the analysis batch?

 

(2)   Therefore, I tried to run without assigning “analysis_batch”, but got an error message
(as attached). How could I solve this exception?

 

Thanks very much for your kindness!

 

Best regards,

Tim

 

From: vijay garla [mailto:vngarla@gmail.com] 
Sent: Friday, June 12, 2015 9:56 AM
To: dev@ctakes.apache.org; tskuo@ucsd.edu
Cc: Vijay Garla
Subject: Re: Question about YTEX

 

You need to annotate some documents with a Collection Processing Engine that stores results
in the YTEX database.   I suggest walking through the fracture demo sample here: https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2.0+-+YTEX+DBCollectionReader

 

-vj

 

On Fri, Jun 12, 2015 at 6:46 PM, Tsung-Ting Kuo <tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>
> wrote:

Hi Vijay,

 

I would like to update my questions:

 

(1)   Auto-complete of concept IDs. I realized that only concepts in the “v_snomed_fword_lookup”
table are usable (e.g., I use “cough” and the auto-complete works as attached).

 

(2)   Clinical document searching. Which table should I use to put the clinical documents
in order to be searchable from the “Semantic Search” function?

 

(3)   Fracture demo. I saw there is a “fracture_demo” table in the YTEX database, how
could I use it in the “Semantic Search” function?

 

Thanks very much!

 

Best regards,

Tim

 

From: Tsung-Ting Kuo [mailto:tskuo@ucsd.edu <mailto:tskuo@ucsd.edu> ] 
Sent: Thursday, June 11, 2015 11:10 AM
To: 'Vijay Garla'
Cc: dev@ctakes.apache.org <mailto:dev@ctakes.apache.org> 


Subject: RE: Question about YTEX

 

Thanks a lot, I followed the instructions and run “ytexweb.sh” script and successfully
run the web app! However, the search cannot return any results (no matter what keyword I type),
and the auto-complete function seems not work. Our experimental website is over here:

 

http://textmining.ucsd.edu:8080/semanticSearch.iface

 

And I also attached the screenshot and the output of the “ytexweb.sh” script. Could you
kindly help to see if there is any setting / configuration needed to be modified in order
to do the search?

 

Thanks very much!

 

Best regards,

Tim

 

From: Vijay Garla [mailto:vijay.garla@yale.edu] 
Sent: Wednesday, June 10, 2015 11:36 PM
To: tskuo@ucsd.edu <mailto:tskuo@ucsd.edu> 
Cc: Vijay Garla; dev@ctakes.apache.org <mailto:dev@ctakes.apache.org> 
Subject: Re: Question about YTEX

 

This is part of the Semantic Similarity Web App.  There is a script to start it; see https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2.0+-+Semantic+Similarity
- just run the ytexweb.sh script in the bin directory

 

 

On Wed, Jun 10, 2015 at 11:32 PM, Tsung-Ting Kuo <tskuo@ucsd.edu <mailto:tskuo@ucsd.edu>
> wrote:

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 <mailto:vijay.garla@yale.edu> ] 
Sent: Wednesday, June 10, 2015 12:10 PM
To: tskuo@ucsd.edu <mailto:tskuo@ucsd.edu> 
Cc: Vijay Garla; dev@ctakes.apache.org <mailto: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
<https://urldefense.proofpoint.com/v2/url?u=https-3A__svn.apache.org_repos_asf_ctakes_trunk_ctakes-2Dytex_scripts_data_mysql_umls_insert-5Fview.template.sql&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=rw3vAb56jh8xMYlMHfE0hS2hfbV3RFxqvusA5jfoLnc&m=ZKgA04a0yvzxPGVaJuAq7iXhdrZStPNaFJYLNpysn_A&s=A4kHSk5EMA2mDAk0zkZPlkPEDsxFWpazfC8SSMzSYDo&e=>


 

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
<https://urldefense.proofpoint.com/v2/url?u=https-3A__code.google.com_p_ytex_wiki_DictionaryLookup-5FV07&d=AwMFaQ&c=-dg2m7zWuuDZ0MUcV7Sdqw&r=rw3vAb56jh8xMYlMHfE0hS2hfbV3RFxqvusA5jfoLnc&m=ZKgA04a0yvzxPGVaJuAq7iXhdrZStPNaFJYLNpysn_A&s=ZmRyuqnM-9FtXw9jKlfrp29gqd-_kd6rjuGSEVEXGgM&e=>
 (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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