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]>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]] > > Sent: Monday, November 26, 2012 12:21 PM > > To: Chen, Pei > > Cc: [email protected]; <[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:ctakes-user-return- > > [email protected]] On Behalf Of Chen, Pei > > Sent: Thursday, November 15, 2012 3:45 PM > > To: <[email protected]> > > Cc: <[email protected]>; [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]> 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:ctakes-user-return-29- > > [email protected] > > > g] On Behalf Of Chen, Pei > > > Sent: Thursday, November 15, 2012 3:15 PM > > > To: <[email protected]> > > > Cc: [email protected]; [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]> 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:ctakes-user-return-26- > > [email protected] > > >> r > > >> g] On Behalf Of Coarr, Matt > > >> Sent: Thursday, November 15, 2012 12:22 PM > > >> To: [email protected] > > >> Cc: [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]> > > 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]> > > 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 > > >>>> > > >>>> > > >> >
