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