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From John Green <john.travis.gr...@gmail.com>
Subject Re: Building
Date Mon, 30 Jun 2014 01:10:12 GMT
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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