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From John Green <john.travis.gr...@gmail.com>
Subject Re: Building
Date Mon, 30 Jun 2014 01:30:58 GMT
Successfully ran command to build the concept graph, however, it seems to
be failing silently. The version issued with ytex is 10m. I expected, worst
case, for mine to be the same, it was 400 bytes (the .gz output). I cant
find anything logged. log4j is complaining it isnt setup correctly,
however, it is directed to the correct config file. Im not familiar with
this logging program, so perhaps the errors are ending up in some kind of
/dev/null.

Also, the web app is only loading sct-msh-csp-aod. I see that in the same
dir there are the others you spoke of. The web app doesnt give an option
for using them (this makes sense as the command line output makes no
mention of loading them) but I can find where what is loaded is defined.

I hope that wasnt too poorly explained,
Thanks,
John


On Sun, Jun 29, 2014 at 9:10 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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