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From Deepal Dhariwal <deepaldhari...@gmail.com>
Subject Re: Regarding Assertion Tagger
Date Fri, 30 Nov 2012 02:46:52 GMT
Hello all,

1. I downloaded ctakes 3.0 and was trying the PAD term Spotter and Drug NER
lookup annotator, but I am getting Resource Initialization Exception.I have
valid UMLS license and I have added username , password in UMLS Lookup
Annotator.   I have been following the thread on PAD Term Spotter bug in
ctakes 2.5 and I wanted to know whether it has been resolved in ctakes 3.0
2. Further my input data set is 4 MB. When I run Collection Processing
Engine on the data set I get java.lang.outofmemory java heap space
exception. Is there any way I could resolve this error and also reduce the
time taken to execute on such huge data set.
3. Lastly as part of my thesis I am working on extracting cardio vascular
terms from medical text using ctakes and umls vocabulary. I want to map
these terms to existing medical owl ontologies for example, UMLS Semantic
Network. I wanted to know whether ctakes community is thinking including
medical ontology feature in ctakes.

Thanks
Deepal Dhariwal


On Mon, Nov 26, 2012 at 12:25 PM, Chen, Pei
<Pei.Chen@childrens.harvard.edu>wrote:

> Thanks Sean,
> If the issue was just a descriptor path issue, then it was probably
> already fixed in 3.0 as part of the ASF move.
> We can just verify and test it?
>
> --Pei
>
> > -----Original Message-----
> > From: Murphy, Sean P. [mailto:Murphy.Sean@mayo.edu]
> > Sent: Monday, November 26, 2012 12:21 PM
> > To: Chen, Pei
> > Cc: ctakes-dev@incubator.apache.org; <ctakes-user@incubator.apache.org>
> > Subject: RE: Regarding Assertion Tagger
> >
> > Hello Pei,
> >       I have created a bug for the 3.0 branch as well.   However, since
> the
> > problem is related to the relative path structures being incorrectly
> migrated
> > to the updated format,  I am not sure if the fix should be made to the
> > sourceforge 2.5 version only or all releases.    The maven driven build
> changes
> > appear to be consolidating some of these issues, but won't be in place
> until
> > the 3.0 build has finalized.    If so, and please correct me if I'm
> wrong, then:
> >       1) There is no need to fix at 2.6. and
> >       2) The fix checked in at 3.0 would be the based on the old
> directory
> > structure.
> >       Thanks,
> >               ~Sean
> >
> > -----Original Message-----
> > From: ctakes-user-return-31-
> > Murphy.Sean=mayo.edu@incubator.apache.org [mailto:ctakes-user-return-
> > 31-Murphy.Sean=mayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
> > Sent: Thursday, November 15, 2012 3:45 PM
> > To: <ctakes-user@incubator.apache.org>
> > Cc: <ctakes-user@incubator.apache.org>; ctakes-dev@incubator.apache.org
> > Subject: Re: Regarding Assertion Tagger
> >
> > There's a 3.0.0 branch.  The release will be made from there.  So we
> should
> > make the fixes in both trunk and 3.0.0.
> >
> >
> > On Nov 15, 2012, at 10:32 PM, "Murphy, Sean P."
> > <Murphy.Sean@mayo.edu> wrote:
> >
> > > Hello Pei,
> > >    The issue is at 2.5.   When is the 3.0 release freeze?   I will try
> to propagate
> > the fix forward.
> > >
> > > -----Original Message-----
> > > From: ctakes-user-return-29-
> > Murphy.Sean=mayo.edu@incubator.apache.org
> > > [mailto:ctakes-user-return-29-
> > Murphy.Sean=mayo.edu@incubator.apache.or
> > > g] On Behalf Of Chen, Pei
> > > Sent: Thursday, November 15, 2012 3:15 PM
> > > To: <ctakes-user@incubator.apache.org>
> > > Cc: ctakes-user@incubator.apache.org; ctakes-dev@incubator.apache.org
> > > Subject: Re: Regarding Assertion Tagger
> > >
> > > Hi Sean,
> > > What was the issue in 2.5?  Just want to make sure this is also fixed
> in the
> > upcoming 3.0 release coming out of ASF as well... Jira#?
> > >
> > >
> > >
> > > On Nov 15, 2012, at 7:59 PM, "Murphy, Sean P."
> > <Murphy.Sean@mayo.edu> wrote:
> > >
> > >> I was able to see an issue with the 'PAD term spotter' which will most
> > likely be related to the problem you're seeing with the smoking status as
> > well.    The problem seems to have  stemmed from the reorganization of
> the
> > path structures with the latest cTAKES  release.  Due to time and
> resource
> > constraints we were not able to test each project independently.
> > >>
> > >> I will open a bug report against these problems and provide a fix as
> soon
> > as possible.  I will keep you posted, but I hope to have this resolved
> in a few
> > days.
> > >>   Thanks,
> > >>       ~Sean
> > >>
> > >> -----Original Message-----
> > >> From: ctakes-user-return-26-
> > Murphy.Sean=mayo.edu@incubator.apache.org
> > >> [mailto:ctakes-user-return-26-
> > Murphy.Sean=mayo.edu@incubator.apache.o
> > >> r
> > >> g] On Behalf Of Coarr, Matt
> > >> Sent: Thursday, November 15, 2012 12:22 PM
> > >> To: ctakes-dev@incubator.apache.org
> > >> Cc: ctakes-user@incubator.apache.org
> > >> Subject: Re: Regarding Assertion Tagger
> > >>
> > >> You were looking in the right place Deepal! The "cTAKES 2.5 Component
> > Use Guide" (the link at the bottom of your email) has a link to more
> > information about the assertion module.
> > >>
> > >> Assertion module info:
> > >>
> > >> https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5+-+Assertion
> > >>
> > >> I'm not familiar with the peripheral artery disease spotter or the
> simulated
> > prod smoking tae.  So I'll let someone else chime in there.
> > >>
> > >> Matt
> > >>
> > >>
> > >> On 2012-11-15 13:11 , "Deepal Dhariwal" <deepaldhariwal@gmail.com>
> > wrote:
> > >>
> > >>> Hello Matt,
> > >>>
> > >>> Thanks for your reply. I am using cTAKES-2.5.0 Binary Version which
> > >>> I have downloaded from
> > >>> https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5+User+Install+Instruc
> > >>> t
> > >>> io
> > >>> ns
> > >>> .
> > >>> I have gone through the cTAKES documentation however no where was
> > it
> > >>> mentioned that polarity / uncertainty properties are on Entity
> Mention.
> > >>> In order to avoid sending repeated mails to the mailing list could
> > >>> you tell me if there is some other documentation as well ? I am
> > >>> trying to use Peripheral Artery Disease Spotter , however it returns
> > >>> only document annotation. Further even the SimulatedProdSmokingTAE
> > >>> Annotator returns smoking status 'unknown' for every input. Is there
> > >>> some order in which these annotator need to be executed (Reference
:
> > >>>
> > https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5+Component+Use+Guide
> > >>> )
> > >>>
> > >>> Thanks for clarifying the user list email id.
> > >>>
> > >>> Regards
> > >>> Deepal Dhariwal
> > >>>
> > >>> On Thu, Nov 15, 2012 at 12:48 PM, Coarr, Matt <mcoarr@mitre.org>
> > wrote:
> > >>>
> > >>>> FYI, the user list is ctakes-user (singular).  I've corrected the
> CC.
> > >>>>
> > >>>> The polarity/conditional/uncertainty properties are on
> > >>>> EntityMention and EventMention.
> > >>>>
> > >>>> Are you using a current development copy of ctakes (from apache
svn
> > >>>> or from 3.0 RC2)?
> > >>>>
> > >>>> If not, what version of ctakes are you using?  Version number?
> > >>>> Binary, source zip, or source from svn?
> > >>>>
> > >>>> Matt
> > >>>>
> > >>>>
> > >>
>

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