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From vijay garla <vnga...@gmail.com>
Subject Re: Question about YTEX
Date Fri, 12 Jun 2015 16:55:45 GMT
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> 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]
> *Sent:* Thursday, June 11, 2015 11:10 AM
> *To:* 'Vijay Garla'
> *Cc:* 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 <vijay.garla@yale.edu>]
> *Sent:* Wednesday, June 10, 2015 11:36 PM
> *To:* tskuo@ucsd.edu
> *Cc:* Vijay Garla; 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> 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]
> *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
> <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> 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]
> *Sent:* Wednesday, June 10, 2015 9:49 AM
> *To:* 'Vijay Garla'; 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 <vijay.garla@yale.edu>]
> *Sent:* Tuesday, June 9, 2015 11:31 PM
> *To:* tskuo@ucsd.edu; dev@ctakes.apache.org
> *Cc:* 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> 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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