I'm using the console version. I suppose the more you add concepts and relation inside the graph the more time the process needs to calculate the similarity. Am I right?
Thanks, Giovanni 2014-11-25 12:48 GMT+01:00 vijay garla <[email protected]>: > You will get a similarity of 0 if one of the concepts isn't in the concept > graph. Did you test this via the web app / rest service / command line? > > YTEX ships with the umls concept graph (all level 0 source vocabs + snomed > ct) and the sct-rxnorm concept graph (snomed-ct + rxnorm) > > When I run the concept similarity service from the command line, I get > these results for umls concept graph: > Concept 1 Concept 2 LCH INTRINSIC_LCH lcs(s) corpus lcs > intrinsic lcs paths > C0042776 C0001175 0.682817 0.261689 > C1140093|C0000000 C1140093 > > C1140093=C0042776->C0029235->*C1140093*<-C0001175<-C0039082<-C0012634|C0000000=C0042776->C0995203->*C0000000*<-C0001175<-C0039082<-C0679227 > > When I run with the sct-umls concept graph: > Concept 1 Concept 2 LCH INTRINSIC_LCH lcs(s) corpus lcs > intrinsic lcs paths > C0042776 C0001175 0.535563 0.267890 C0000000 > C0000000 > > C0000000=C0042776->C0445623->C0029235->C2720507->*C0000000*<-C0001175<-C0729529<-C0153114 > > Here is my command: > java -cp %CLASSPATH% > -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xmx2g > -Dytex.conceptGraphName=umls > org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl -concepts > C0042776,C0001175 -lcs -metrics LCH,INTRINSIC_LCH > or > java -cp %CLASSPATH% > -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xmx2g > -Dytex.conceptGraphName=sct-umls > org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl -concepts > C0042776,C0001175 -lcs -metrics LCH,INTRINSIC_LCH > > If you add the -lcs option you will get all the paths. > > I think the high similarity you expect may not be modeled in the graph - > *AIDS* is a disease, *HIV* is-a *Virus* (that *causes AIDS*). I'm not > sure if you can view *causes *as a hierarchical relationship. If you > want to, you can create a concept graph that includes additional > relationships (you would have to check to see if this relationship is > modeled in the UMLS). > > HTH, > > VJ > > > > On Mon, Nov 24, 2014 at 7:55 PM, Giovanni Di Santo < > [email protected]> wrote: > >> The installation procedure is over now and it seems it went well. If you >> need I can provide the installation logs. >> I have some questions about the semantic similarity feature. I have tried >> the example provided in the guide and It worked. I tried with other cui for >> example virus(C0042776) and aids(C0001175) and it gave me a similarity of >> 0.0... that sounded strange. >> I thought maybe because I was using a small part of umls so I tried with >> the option "-Dytex.conceptGraphName=umls" but I got the same result. >> Do I have to build my own concept graph and corups information content as >> described in the guide? if yes how can I do that for the whole umls >> database? Do you think the final graph would be too big? >> >> Best regards, >> >> Giovanni >> >> 2014-11-24 16:49 GMT+01:00 Giovanni Di Santo <[email protected]>: >> >>> Hi Vijay, >>> Thanks for your reply. >>> I added that file as you suggested. The installation process has passed >>> that point and now... I suppose... It's filling the database. I have been >>> running it for 2 hours so far... I suppose it's taking a lot of time cause >>> it's creating a dictionary lookup table for my local umls installation. >>> I'll let you know when the installation is over. >>> >>> Best regards >>> >>> Giovanni >>> >>> 2014-11-24 13:45 GMT+01:00 vijay garla <[email protected]>: >>> >>>> Hi Giovanni, >>>> >>>> I think I found a bug in the offending class. Can you copy the >>>> attached file to this directory: >>>> >>>> YTEX_HOME\resources\org\apache\ctakes\ytex\ >>>> >>>> And retry? >>>> >>>> Thanks! >>>> >>>> VJ >>>> >>>> >>>> On Thu, Nov 20, 2014 at 4:16 PM, Giovanni Di Santo < >>>> [email protected]> wrote: >>>> >>>>> Hi, >>>>> I have tried to install YTEX in another machine and the same exception >>>>> is thrown during the installation. The output is slightly different: >>>>> http://pastebin.com/gVhSFYKp. >>>>> I suppose I make some mistakes during the installation process. >>>>> When in the ytes installation guide is written to copy "over" my >>>>> installation I use a command like "cp -R /directory_fo_copy/* >>>>> /ctakes_home". >>>>> Is there any already ready ytex version that I can download and use >>>>> for Linux? >>>>> >>>>> I don't really now what could be the problem and I need to test the >>>>> Semantic Similarity feature. >>>>> >>>>> Best regards >>>>> >>>>> Giovanni >>>>> >>>>> 2014-11-12 0:05 GMT+01:00 Kim Ebert <[email protected]>: >>>>> >>>>>> Adding developer mailing list, as I'm not sure what is causing your >>>>>> error. >>>>>> >>>>>> Kim Ebert >>>>>> 1.801.669.7342 >>>>>> Perfect Search Corp >>>>>> http://www.perfectsearchcorp.com/ >>>>>> >>>>>> On 10/29/2014 11:57 AM, Giovanni Di Santo wrote: >>>>>> > Hi, >>>>>> > I'm trying to install ytex. I've followed the instructions provided >>>>>> > here >>>>>> > >>>>>> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation >>>>>> > but the installing process stops and raises an Excpetion >>>>>> > java.lang.ExceptionInInitializerError. >>>>>> > More precisely I receive that output: http://pastebin.com/PrWyBxhx >>>>>> . >>>>>> > I'm using cTakes 3.2 and the I've installed locally on a mysql db >>>>>> the >>>>>> > umls 2014AA version. >>>>>> > >>>>>> > Best regards, >>>>>> > >>>>>> > Giovanni >>>>>> >>>>>> >>>>> >>>> >>> >> >
