Once a concept graph is loaded, calculating the similarity is pretty quick. the larger the concept graph, the longer it takes to load, and the more memory is required.
-vj On Wed, Nov 26, 2014 at 10:07 AM, Giovanni Di Santo <[email protected] > wrote: > 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 >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>> >> >
