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 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 For more detail on how this works, see https://code.google.com/p/ytex/wiki/DictionaryLookup_V07 (docs slightly out of date).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 > > > > >
