Correction: "cant find where what is loaded is defined".
On Sun, Jun 29, 2014 at 9:30 PM, John Green <[email protected]> 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 <[email protected]> > 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 <[email protected]> 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 <[email protected] >>> > >>> 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 >>> >> >> >
