Deepal,
Thanks for verifying #1. It took a bit longer to setup my
environment on a test machine to verify, but please bear with me while I run
through a regime of tests regarding these pipelines.
#2. You may need to increase the pool size used by the VM arguments for your
java environment. I believe the default is " -Xms1024M -Xmx2048M". If your
system has the resources you may want to increase these by 1GM and retest. I
do not believe this will improve the time to run, however. Perhaps someone
else has some suggestions regarding this aspect(?).
#3. I will have to defer this question to the rest of the team.
From: Deepal Dhariwal [mailto:[email protected]]
Sent: Thursday, November 29, 2012 8:47 PM
To: [email protected]
Cc: Murphy, Sean P.; <[email protected]>
Subject: Re: Regarding Assertion Tagger
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
<[email protected]<mailto:[email protected]>> 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:[email protected]<mailto:[email protected]>]
> Sent: Monday, November 26, 2012 12:21 PM
> To: Chen, Pei
> Cc: [email protected]<mailto:[email protected]>;
> <[email protected]<mailto:[email protected]>>
> 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-
> [email protected]<mailto:[email protected]>
> [mailto:ctakes-user-return-<mailto:ctakes-user-return->
> [email protected]<mailto:[email protected]>]
> On Behalf Of Chen, Pei
> Sent: Thursday, November 15, 2012 3:45 PM
> To:
> <[email protected]<mailto:[email protected]>>
> Cc:
> <[email protected]<mailto:[email protected]>>;
> [email protected]<mailto:[email protected]>
> 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."
> <[email protected]<mailto:[email protected]>> 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-
> [email protected]<mailto:[email protected]>
> > [mailto:ctakes-user-return-29-<mailto:ctakes-user-return-29->
> [email protected]<mailto:[email protected]>
> > g] On Behalf Of Chen, Pei
> > Sent: Thursday, November 15, 2012 3:15 PM
> > To:
> > <[email protected]<mailto:[email protected]>>
> > Cc:
> > [email protected]<mailto:[email protected]>;
> > [email protected]<mailto:[email protected]>
> > 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."
> <[email protected]<mailto:[email protected]>> 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-
> [email protected]<mailto:[email protected]>
> >> [mailto:ctakes-user-return-26-<mailto:ctakes-user-return-26->
> [email protected]<mailto:[email protected]>
> >> r
> >> g] On Behalf Of Coarr, Matt
> >> Sent: Thursday, November 15, 2012 12:22 PM
> >> To: [email protected]<mailto:[email protected]>
> >> Cc:
> >> [email protected]<mailto:[email protected]>
> >> 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"
> >> <[email protected]<mailto:[email protected]>>
> 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
> >>> <[email protected]<mailto:[email protected]>>
> 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
> >>>>
> >>>>
> >>
