The ytexWeb application tries to look up concepts from terms using the ytex dictionary lookup table, which is a small subset of the UMLS. Can you try specifying cuis? That skips the lookup - if the concepts are in the concept graph, this will work.
Best, vj On Sun, Jun 29, 2014 at 6:10 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 > > >
