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 <[email protected]> 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:[email protected]] > *Sent:* Thursday, June 11, 2015 11:10 AM > *To:* 'Vijay Garla' > *Cc:* [email protected] > > *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:[email protected] <[email protected]>] > *Sent:* Wednesday, June 10, 2015 11:36 PM > *To:* [email protected] > *Cc:* Vijay Garla; [email protected] > *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 <[email protected]> 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:[email protected]] > *Sent:* Wednesday, June 10, 2015 12:10 PM > *To:* [email protected] > *Cc:* Vijay Garla; [email protected] > > > *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 <[email protected]> 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:[email protected]] > *Sent:* Wednesday, June 10, 2015 9:49 AM > *To:* 'Vijay Garla'; [email protected] > *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:[email protected] <[email protected]>] > *Sent:* Tuesday, June 9, 2015 11:31 PM > *To:* [email protected]; [email protected] > *Cc:* [email protected] > *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 <[email protected]> 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 > > > > > > > > >
