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From John Green <john.travis.gr...@gmail.com>
Subject Re: Building
Date Tue, 15 Jul 2014 00:11:22 GMT
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 <vngarla@gmail.com> wrote:

> When you run the webapp, the restful sevices run as well
>
> On Friday, July 4, 2014, John Green <john.travis.green@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 <vngarla@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.green@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 <vngarla@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.green@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
> > > > >
> > > >
> > >
> >
>

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