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From John Green <john.travis.gr...@gmail.com>
Subject Re: Building
Date Mon, 30 Jun 2014 01:31:55 GMT
Correction: "cant find where what is loaded is defined".


On Sun, Jun 29, 2014 at 9:30 PM, John Green <john.travis.green@gmail.com>
wrote:

> 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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