Hi Vijay, Would you happen to have chance to take a look and give me some suggestions about the fracture demo?
Thanks very much! Best regards, Tim > On Jun 12, 2015, at 10:32 AM, Tsung-Ting Kuo <[email protected]> wrote: > > 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:[email protected] <mailto:[email protected]>] > Sent: Friday, June 12, 2015 9:56 AM > To: [email protected] <mailto:[email protected]>; [email protected] > <mailto:[email protected]> > 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 > > <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] > <mailto:[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] <mailto:[email protected]>] >> Sent: Thursday, June 11, 2015 11:10 AM >> To: 'Vijay Garla' >> Cc: [email protected] <mailto:[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 >> <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] >> <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 >> >> <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] >>>> <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 >>>>> >>>> >>>> >>> >>> >> >> > > > <cpe.out>
