the concept graph used by the webapp is defined in ytex.properties. You can also override it using the ytex.conceptGraph system property (add -Dytex.conceptGraph=xxx to the beginning of the ytexweb.bat java command line).
I'm not sure about why you don't see any log output: when I run this line specifying an invalid concept graph name: java -cp %CLASSPATH% -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xmx1g org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl -name <concept graph name>C:\java\apache-ctakes-3.1.2-SNAPSHOT>java -cp %CLASSPATH% -Dlog4j.configuration= file:/%CTAKES_HOME%/config/log4j.xml -Xmx1g org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl -name test I get this output (indicating that the corresponding properties file can't be found): log4j: reset attribute= "false". log4j: Threshold ="null". log4j: Level value for root is [INFO]. log4j: root level set to INFO log4j: Class name: [org.apache.log4j.ConsoleAppender] log4j: Parsing layout of class: "org.apache.log4j.PatternLayout" log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss} %5p %c{1} - %m%n]. log4j: Adding appender named [consoleAppender] to category [root]. *properties file could not be located: org/apache/ctakes/ytex/conceptGraph/test.xml * If you're on linux, can you play around with the file url for log4j? Best, VJ On Sun, Jun 29, 2014 at 6:30 PM, John Green <john.travis.gr...@gmail.com> wrote: > Successfully ran command to build the concept graph, however, it seems to > be failing silently. The version issued with ytex is 10m. I expected, worst > case, for mine to be the same, it was 400 bytes (the .gz output). I cant > find anything logged. log4j is complaining it isnt setup correctly, > however, it is directed to the correct config file. Im not familiar with > this logging program, so perhaps the errors are ending up in some kind of > /dev/null. > > Also, the web app is only loading sct-msh-csp-aod. I see that in the same > dir there are the others you spoke of. The web app doesnt give an option > for using them (this makes sense as the command line output makes no > mention of loading them) but I can find where what is loaded is defined. > > I hope that wasnt too poorly explained, > Thanks, > John > > > On Sun, Jun 29, 2014 at 9:10 PM, John Green <john.travis.gr...@gmail.com> > wrote: > > > Hi Vijay, thank you for your time. > > > > Your documentation was quite good. I had no problem setting up ytex with > > UMLS running on my local mysql server. Where I ran into problems was > > understanding how to launch the web service (also, is there anyway to run > > this in a RESTful mode? Btw, the informatics.yale links returns 502). > After > > I did get it launched, and the confusion was probably all my fault, the > > concepts available to the similarity fields seemed very sparse; I just > > started typing randomly, hematochezia, choledocholithiasis, etc, and > > nothing would come up. The best I got was gallbladder function test, > which, > > if Im understanding it right, would be an alkphos, but alkaline > phosphatase > > didnt come up, which led to me to believe they were smaller sets of the > the > > snomed, mesh, etc compilations (as I checked the UMLS db and these > concepts > > are there). > > > > I think I got that execution command from the code.google, which is > > probably why it was stale. I did not see the ytex semantic similarity > guide > > under the ctakes components part (sorry, thanks for pointing me there, > ill > > get to work on reading it). > > > > So bottom line: are the ones that shipped watered down versions? And if > > not, why are my concepts coming up short? If you give me a hint at where > to > > check Ill investigate. > > > > Thanks! > > JG > > > > > > On Sun, Jun 29, 2014 at 8:56 PM, vijay garla <vnga...@gmail.com> wrote: > > > >> Hi John, > >> > >> YTEX ships with 3 concept graphs (see > >> > >> > https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1.2+-+Semantic+Similarity > >> ): > >> > >> - sct-rxnorm: concepts from SNOMED-CT and RXNORM. This is the > default. > >> - sct-msh-csp-aod: concepts from the SNOMED-CT, MeSH, CRISP, and > >> Alcohol > >> and Drug thesaurus > >> - umls: concepts from all restriction free (level 0) UMLS source > >> vocabularies and SNOMED-CT > >> > >> > >> These concept graphs are included in ytex resources zip (see > >> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation): > >> 3) Unzip YTEX Resources (Optional - UTS login required) > >> > >> Download and unzip ctakes-ytex-resources-3.1.2-SNAPSHOT.zip > >> < > >> > http://www.ytex-nlp.org/umls.download/secure/3.1/ctakes-ytex-resources-3.1.2-SNAPSHOT.zip > >> > > >> 'over' > >> your installation. This contains: > >> > >> - Concept Graphs derived from the UMLS2013AA used to compute semantic > >> similarity measures > >> > >> > >> > >> All YTEX packages moved from the ytex namespace into > >> org.apache.ctakes.ytex > >> - can you tell me which document you were looking at that mentioned > >> ytex.kernel.dao.ConceptDaoImpl? I thought I had fixed this in the > >> documentation. > >> > >> HTH, > >> > >> -vj > >> > >> > >> On Sun, Jun 29, 2014 at 2:25 PM, John Green < > john.travis.gr...@gmail.com> > >> wrote: > >> > >> > I got the semantic similarity web app running in ytex. Im still > learning > >> > umls terminology, but I believe it says that out of the box its > concept > >> > graphs are limited to the free set from umls? Does this mean without > >> > permissions? Similar to ctakes with umls rights? The concepts > available > >> > seem limited so this would make sense. > >> > > >> > So, to take full advantage I would need to rebuild the concept graph, > >> > correct? Im in the process of doing this but getting classpath > errors. I > >> > used java a bit ten years ago, so you can probably guess these will > >> take me > >> > a minute to resolve. Notably, it is complaining about > >> > ytex.kernel.dao.ConceptDaoImpl. > >> > > >> > > >> > Thanks all, > >> > > >> > > >> > JG > >> > > >> > — > >> > Sent from Mailbox for iPhone > >> > > > > >