ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From vijay garla <vnga...@gmail.com>
Subject Re: Building
Date Thu, 03 Jul 2014 02:58:54 GMT
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
> >
>

Mime
  • Unnamed multipart/alternative (inline, None, 0 bytes)
View raw message