ctakes-user mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
From Giovanni Di Santo <giovi.disa...@gmail.com>
Subject Re: YTEX installation Exception java.lang.ExceptionInInitializerError
Date Wed, 26 Nov 2014 09:07:53 GMT
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
>>>>>>
>>>>>>
>>>>>
>>>>
>>>
>>
>

Mime
View raw message