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From vijay garla <vnga...@gmail.com>
Subject Re: YTEX installation Exception java.lang.ExceptionInInitializerError
Date Wed, 26 Nov 2014 10:12:14 GMT
Once a concept graph is loaded, calculating the similarity is pretty quick.
 the larger the concept graph, the longer it takes to load, and the more
memory is required.

-vj

On Wed, Nov 26, 2014 at 10:07 AM, Giovanni Di Santo <giovi.disanto@gmail.com
> wrote:

> I'm using the console version. I suppose the more you add concepts and
> relation inside the graph the more time the process needs to calculate the
> similarity. Am I right?
>
> Thanks,
>
> Giovanni
>
> 2014-11-25 12:48 GMT+01:00 vijay garla <vngarla@gmail.com>:
>
>> You will get a similarity of 0 if one of the concepts isn't in the
>> concept graph.  Did you test this via the web app / rest service / command
>> line?
>>
>> YTEX ships with the umls concept graph (all level 0 source vocabs +
>> snomed ct) and the sct-rxnorm concept graph (snomed-ct + rxnorm)
>>
>> When I run the concept similarity service from the command line, I get
>> these results for umls concept graph:
>> Concept 1       Concept 2       LCH     INTRINSIC_LCH   lcs(s)  corpus
>> lcs intrinsic lcs   paths
>> C0042776        C0001175        0.682817        0.261689
>>  C1140093|C0000000               C1140093
>>  C1140093=C0042776->C0029235->*C1140093*<-C0001175<-C0039082<-C0012634|C0000000=C0042776->C0995203->*C0000000*<-C0001175<-C0039082<-C0679227
>>
>> When I run with the sct-umls concept graph:
>> Concept 1       Concept 2       LCH     INTRINSIC_LCH   lcs(s)  corpus
>> lcs intrinsic lcs   paths
>> C0042776        C0001175        0.535563        0.267890        C0000000
>>         C0000000
>>  C0000000=C0042776->C0445623->C0029235->C2720507->*C0000000*<-C0001175<-C0729529<-C0153114
>>
>> Here is my command:
>> java -cp %CLASSPATH%
>> -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xmx2g
>>  -Dytex.conceptGraphName=umls
>> org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl -concepts
>> C0042776,C0001175 -lcs  -metrics LCH,INTRINSIC_LCH
>> or
>> java -cp %CLASSPATH%
>> -Dlog4j.configuration=file:/%CTAKES_HOME%/config/log4j.xml -Xmx2g
>>  -Dytex.conceptGraphName=sct-umls
>> org.apache.ctakes.ytex.kernel.metric.ConceptSimilarityServiceImpl -concepts
>> C0042776,C0001175 -lcs  -metrics LCH,INTRINSIC_LCH
>>
>> If you add the -lcs option you will get all the paths.
>>
>> I think the high similarity you expect may not be modeled in the graph -
>> *AIDS* is a disease, *HIV* is-a *Virus* (that *causes AIDS*).  I'm not
>> sure if you can view *causes *as a hierarchical relationship.  If you
>> want to, you can create a concept graph that includes additional
>> relationships (you would have to check to see if this relationship is
>> modeled in the UMLS).
>>
>> HTH,
>>
>> VJ
>>
>>
>>
>> On Mon, Nov 24, 2014 at 7:55 PM, Giovanni Di Santo <
>> giovi.disanto@gmail.com> wrote:
>>
>>> The installation procedure is over now and it seems it went well. If you
>>> need I can provide the installation logs.
>>> I have some questions about the semantic similarity feature. I have
>>> tried the example provided in the guide and It worked. I tried with other
>>> cui for example virus(C0042776) and aids(C0001175) and it gave me a
>>> similarity of 0.0... that sounded strange.
>>> I thought maybe because I was using a small part of umls so I tried with
>>> the option "-Dytex.conceptGraphName=umls" but I got the same result.
>>> Do I have to build my own concept graph and corups information content
>>> as described in the guide? if yes how can I do that for the whole umls
>>> database? Do you think the final graph would be too big?
>>>
>>> Best regards,
>>>
>>> Giovanni
>>>
>>> 2014-11-24 16:49 GMT+01:00 Giovanni Di Santo <giovi.disanto@gmail.com>:
>>>
>>>> Hi Vijay,
>>>> Thanks for your reply.
>>>> I added that file as you suggested. The installation process has passed
>>>> that point and now... I suppose... It's filling the database. I have been
>>>> running it for 2 hours so far... I suppose it's taking a lot of time cause
>>>> it's creating a dictionary lookup table for my local umls installation.
>>>> I'll let you know when the installation is over.
>>>>
>>>> Best regards
>>>>
>>>> Giovanni
>>>>
>>>> 2014-11-24 13:45 GMT+01:00 vijay garla <vngarla@gmail.com>:
>>>>
>>>>> Hi Giovanni,
>>>>>
>>>>> I think I found a bug in the offending class.  Can you copy the
>>>>> attached file to this directory:
>>>>>
>>>>> YTEX_HOME\resources\org\apache\ctakes\ytex\
>>>>>
>>>>> And retry?
>>>>>
>>>>> Thanks!
>>>>>
>>>>> VJ
>>>>>
>>>>>
>>>>> On Thu, Nov 20, 2014 at 4:16 PM, Giovanni Di Santo <
>>>>> giovi.disanto@gmail.com> wrote:
>>>>>
>>>>>> Hi,
>>>>>> I have tried to install YTEX in another machine and the same
>>>>>> exception is thrown during the installation. The output is slightly
>>>>>> different: http://pastebin.com/gVhSFYKp.
>>>>>> I suppose I make some mistakes during the installation process.
>>>>>> When in the ytes installation guide is written to copy  "over" my
>>>>>> installation I use a command like "cp -R /directory_fo_copy/* /ctakes_home".
>>>>>> Is there any already ready ytex version that I can download and use
>>>>>> for Linux?
>>>>>>
>>>>>> I don't really now what could be the problem and I need to test the
>>>>>> Semantic Similarity feature.
>>>>>>
>>>>>> Best regards
>>>>>>
>>>>>> Giovanni
>>>>>>
>>>>>> 2014-11-12 0:05 GMT+01:00 Kim Ebert <kim.ebert@perfectsearchcorp.com>
>>>>>> :
>>>>>>
>>>>>>> Adding developer mailing list, as I'm not sure what is causing
your
>>>>>>> error.
>>>>>>>
>>>>>>> Kim Ebert
>>>>>>> 1.801.669.7342
>>>>>>> Perfect Search Corp
>>>>>>> http://www.perfectsearchcorp.com/
>>>>>>>
>>>>>>> On 10/29/2014 11:57 AM, Giovanni Di Santo wrote:
>>>>>>> > Hi,
>>>>>>> > I'm trying to install ytex. I've followed the instructions
provided
>>>>>>> > here
>>>>>>> >
>>>>>>> https://cwiki.apache.org/confluence/display/CTAKES/YTEX+Installation
>>>>>>> > but the installing process stops and raises an Excpetion
>>>>>>> > java.lang.ExceptionInInitializerError.
>>>>>>> > More precisely I receive that output: http://pastebin.com/PrWyBxhx
>>>>>>> .
>>>>>>> > I'm using cTakes 3.2 and the I've installed locally on a
mysql db
>>>>>>> the
>>>>>>> > umls 2014AA version.
>>>>>>> >
>>>>>>> > Best regards,
>>>>>>> >
>>>>>>> > Giovanni
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

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