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From John Green <john.travis.gr...@gmail.com>
Subject Re: Building
Date Fri, 04 Jul 2014 12:03:26 GMT
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 <vngarla@gmail.com> 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.green@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 <vngarla@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.green@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
> > >
> >
>

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