Hi Vijay - The queries are all returning odd errors but the commands to list what graphs are available. I will try and sleuth out a better report than that.
Thank you for your continued help, JG On Sat, Jul 5, 2014 at 12:53 AM, vijay garla <vnga...@gmail.com> wrote: > When you run the webapp, the restful sevices run as well > > On Friday, July 4, 2014, John Green <john.travis.gr...@gmail.com> wrote: > > > Vijay - Ha! Ok. Works perfect with cuis. > > > > Is there a way to run the web application as a RESTful API? You mention > > this as a service on your yale box, but I dont see a way to deploy it > this > > way local. > > > > Thanks again, > > JG > > > > > > On Wed, Jul 2, 2014 at 10:58 PM, vijay garla <vnga...@gmail.com > > <javascript:;>> wrote: > > > > > 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 > > <javascript:;>> > > > 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 > > <javascript:;>> 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 <javascript:;> > > > > > > > > > > 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 > > > > > > > > > > > > > > >
