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From vijay garla <vnga...@gmail.com>
Subject Re: Building
Date Thu, 03 Jul 2014 02:56:35 GMT
the concept graph used by the webapp is defined in ytex.properties.  You
can also override it using the ytex.conceptGraph system property (add
-Dytex.conceptGraph=xxx to the beginning of the ytexweb.bat java command
line).

I'm not sure about why you don't see any log output:
when I run this line specifying an invalid concept graph name:
java -cp %CLASSPATH% -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml
-Xmx1g org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl -name <concept
graph name>C:\java\apache-ctakes-3.1.2-SNAPSHOT>java -cp %CLASSPATH%
-Dlog4j.configuration=
file:/%CTAKES_HOME%/config/log4j.xml -Xmx1g
org.apache.ctakes.ytex.kernel.dao.ConceptDaoImpl -name test

I get this output (indicating that the corresponding properties file can't
be found):
log4j: reset attribute= "false".
log4j: Threshold ="null".
log4j: Level value for root is  [INFO].
log4j: root level set to INFO
log4j: Class name: [org.apache.log4j.ConsoleAppender]
log4j: Parsing layout of class: "org.apache.log4j.PatternLayout"
log4j: Setting property [conversionPattern] to [%d{dd MMM yyyy HH:mm:ss}
%5p %c{1} - %m%n].
log4j: Adding appender named [consoleAppender] to category [root].
*properties file could not be located:
org/apache/ctakes/ytex/conceptGraph/test.xml *

If you're on linux, can you play around with the file url for log4j?

Best,

VJ


On Sun, Jun 29, 2014 at 6:30 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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