Return-Path: X-Original-To: apmail-incubator-ctakes-user-archive@minotaur.apache.org Delivered-To: apmail-incubator-ctakes-user-archive@minotaur.apache.org Received: from mail.apache.org (hermes.apache.org [140.211.11.3]) by minotaur.apache.org (Postfix) with SMTP id 164A0E7A9 for ; Fri, 30 Nov 2012 20:10:46 +0000 (UTC) Received: (qmail 7765 invoked by uid 500); 30 Nov 2012 20:10:45 -0000 Delivered-To: apmail-incubator-ctakes-user-archive@incubator.apache.org Received: (qmail 7731 invoked by uid 500); 30 Nov 2012 20:10:44 -0000 Mailing-List: contact ctakes-user-help@incubator.apache.org; run by ezmlm Precedence: bulk List-Help: List-Unsubscribe: List-Post: List-Id: Reply-To: ctakes-user@incubator.apache.org Delivered-To: mailing list ctakes-user@incubator.apache.org Received: (qmail 7714 invoked by uid 99); 30 Nov 2012 20:10:44 -0000 Received: from nike.apache.org (HELO nike.apache.org) (192.87.106.230) by apache.org (qpsmtpd/0.29) with ESMTP; Fri, 30 Nov 2012 20:10:44 +0000 X-ASF-Spam-Status: No, hits=-0.1 required=5.0 tests=HTML_MESSAGE,RCVD_IN_DNSWL_MED,SPF_PASS X-Spam-Check-By: apache.org Received-SPF: pass (nike.apache.org: local policy) Received: from [129.176.212.47] (HELO mail10.mayo.edu) (129.176.212.47) by apache.org (qpsmtpd/0.29) with ESMTP; Fri, 30 Nov 2012 20:10:35 +0000 X-IronPort-AV: E=McAfee;i="5400,1158,6912"; a="194847707" Received: from roedlp004a.mayo.edu (HELO mail10.mayo.edu) ([129.176.158.14]) by ironport10-dlp.mayo.edu with ESMTP; 30 Nov 2012 14:10:12 -0600 X-IronPort-Anti-Spam-Filtered: true X-IronPort-Anti-Spam-Result: AgEFANIRuVCBsNQ1/2dsb2JhbABEgkm9NhZzgh4BAQEEGg0GHCUXBAIBCBEEAQEBCg4IAQYHIREUCQgBAQQBEggMh2oDDwy2Gg1MiQQEi1dpC4ERgkRhA5JOgV2NCYUQgnKBbDU X-IronPort-AV: E=McAfee;i="5400,1158,6912"; a="194847704" Received: from mhro1a.mayo.edu ([129.176.212.53]) by ironport10.mayo.edu with ESMTP; 30 Nov 2012 14:10:11 -0600 Received: from MSGPEXCHA07A.mfad.mfroot.org (msgpexcha07a.mayo.edu [129.176.249.223]) by mhro1a.mayo.edu with ESMTP id BT-MMP-3886264; Fri, 30 Nov 2012 14:10:11 -0600 Received: from MSGPEXCEI11A.mfad.mfroot.org ([169.254.5.196]) by MSGPEXCHA07A.mfad.mfroot.org ([169.254.10.31]) with mapi id 14.02.0309.002; Fri, 30 Nov 2012 14:10:11 -0600 From: "Murphy, Sean P." To: "ctakes-user@incubator.apache.org" , 'Deepal Dhariwal' , "'ctakes-dev@incubator.apache.org'" Subject: RE: DrugNER & PAD Term Spotter (was: Regarding Assertion Tagger) Thread-Topic: DrugNER & PAD Term Spotter (was: Regarding Assertion Tagger) Thread-Index: Ac3PKWtL6l9yelA0SE6W8uSDx58ZwwADGjUw Date: Fri, 30 Nov 2012 20:10:10 +0000 Message-ID: <38DD5510DD255845934ABD523985843B035485@MSGPEXCEI11A.mfad.mfroot.org> References: <924DE05C19409B438EB81DE683A942D923E17F@CHEXMBX1A.CHBOSTON.ORG> In-Reply-To: <924DE05C19409B438EB81DE683A942D923E17F@CHEXMBX1A.CHBOSTON.ORG> Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: x-originating-ip: [10.128.209.28] Content-Type: multipart/alternative; boundary="_000_38DD5510DD255845934ABD523985843B035485MSGPEXCEI11Amfadm_" MIME-Version: 1.0 X-CFilter-Loop: Reflected X-Virus-Checked: Checked by ClamAV on apache.org --_000_38DD5510DD255845934ABD523985843B035485MSGPEXCEI11Amfadm_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Thanks Pei, Agreed. I believe there was an ant build script built by o= ur team that provided an automated means to change the locations when creat= ing the iCTAKES build from the separate cTAKES projects. I wasn't sure t= he nature of the changes to the Maven driven builds, so that's where I misu= nderstood where and how the changes were to be made. If okay with everyone I will search all the projects using = the old implementation of the import location relative paths, update and te= st against 3.0. Thanks, ~Sean From: ctakes-user-return-39-Murphy.Sean=3Dmayo.edu@incubator.apache.org [ma= ilto:ctakes-user-return-39-Murphy.Sean=3Dmayo.edu@incubator.apache.org] On = Behalf Of Chen, Pei Sent: Friday, November 30, 2012 12:55 PM To: ctakes-user@incubator.apache.org; 'Deepal Dhariwal'; 'ctakes-dev@incuba= tor.apache.org' Subject: RE: DrugNER & PAD Term Spotter (was: Regarding Assertion Tagger) Hi Sean, It should load the type system by name instead of path now. The xml file should: Instead of: While testing this, I also noticed that the chunker classname in DrugAggreg= atePlaintextProcessor.xml should be: org.apache.ctakes.chunker.ae.PhraseTypeChunkCreator instead of: edu.mayo.bmi.uima.chunker.PhraseTypeChunkCreator --Pei From: Murphy, Sean P. [mailto:Murphy.Sean@mayo.edu] Sent: Friday, November 30, 2012 1:13 PM To: 'Deepal Dhariwal'; 'ctakes-dev@incubator.apache.org' Cc: '>' Subject: RE: Regarding Assertion Tagger I'm able to reproduce the problem on 3.0 in either the prebuild zip bin or = the Maven built environment. The underlying issue appears to be related to= the paths not being correctly handled. I will investigate further. Caused by: org.apache.uima.util.InvalidXMLException: Import failed. Could = not read from URL file:/C:/tools/cTAKESv3.0_bin/desc/ctakes-drug-ner/desc/t= ype_system/NERTypeSystem.xml. (Descriptor: file:/C:/tools/cTAKESv3.0_bin/de= sc/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml) at org.apache.uima.resource.metadata.impl.TypeSystemDescrip= tion_impl.resolveImports(TypeSystemDescription_impl.java:231) at org.apache.uima.resource.metadata.impl.TypeSystemDescrip= tion_impl.resolveImports(TypeSystemDescription_impl.java:207) at org.apache.uima.analysis_engine.metadata.impl.AnalysisEn= gineMetaData_impl.resolveImports(AnalysisEngineMetaData_impl.java:87) at org.apache.uima.analysis_engine.impl.AnalysisEngineDescr= iption_impl.resolveImports(AnalysisEngineDescription_impl.java:741) at org.apache.uima.analysis_engine.impl.AnalysisEngineDescr= iption_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_= impl.java:827) at org.apache.uima.analysis_engine.impl.AnalysisEngineDescr= iption_impl.resolveImports(AnalysisEngineDescription_impl.java:733) at org.apache.uima.analysis_engine.impl.AnalysisEngineDescr= iption_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_= impl.java:827) at org.apache.uima.analysis_engine.impl.AnalysisEngineDescr= iption_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_= impl.java:765) at org.apache.uima.analysis_engine.impl.AnalysisEngineDescr= iption_impl.getDelegateAnalysisEngineSpecifiers(AnalysisEngineDescription_i= mpl.java:193) at org.apache.uima.analysis_engine.impl.AggregateAnalysisEn= gine_impl.initialize(AggregateAnalysisEngine_impl.java:147) ... 45 more Caused by: java.io.FileNotFoundException: C:\tools\cTAKESv3.0_bin\desc\ctak= es-drug-ner\desc\type_system\NERTypeSystem.xml (The system cannot find the = path specified) at java.io.FileInputStream.open(Native Method) at java.io.FileInputStream.(Unknown Source) at java.io.FileInputStream.(Unknown Source) at sun.net.www.protocol.file.FileURLConnection.connect(Unkn= own Source) at sun.net.www.protocol.file.FileURLConnection.getInputStre= am(Unknown Source) at org.apache.uima.util.XMLInputSource.(XMLInputSourc= e.java:120) at org.apache.uima.resource.metadata.impl.TypeSystemDescrip= tion_impl.resolveImport(TypeSystemDescription_impl.java:263) at org.apache.uima.resource.metadata.impl.TypeSystemDescrip= tion_impl.resolveImports(TypeSystemDescription_impl.java:229) ... 54 more Thanks, ~Sean From: Murphy, Sean P. Sent: Friday, November 30, 2012 8:58 AM To: 'Deepal Dhariwal'; ctakes-dev@incubator.apache.org Cc: > Subject: RE: Regarding Assertion Tagger 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 ru= n through a regime of tests regarding these pipelines. #2. You may need to increase the pool size used by the VM arguments for you= r java environment. I believe the default is " -Xms1024M -Xmx2048M". If = your system has the resources you may want to increase these by 1GM and ret= est. I do not believe this will improve the time to run, however. Perha= ps 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:deepaldhariwal@gmail.com] Sent: Thursday, November 29, 2012 8:47 PM To: ctakes-dev@incubator.apache.org Cc: Murphy, Sean P.; > 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 hav= e valid UMLS license and I have added username , password in UMLS Lookup An= notator. I have been following the thread on PAD Term Spotter bug in ctak= es 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 Engi= ne on the data set I get java.lang.outofmemory java heap space exception. I= s there any way I could resolve this error and also reduce the time taken t= o execute on such huge data set. 3. Lastly as part of my thesis I am working on extracting cardio vascular t= erms from medical text using ctakes and umls vocabulary. I want to map thes= e terms to existing medical owl ontologies for example, UMLS Semantic Netwo= rk. 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 > 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; > > Subject: RE: Regarding Assertion Tagger > > Hello Pei, > I have created a bug for the 3.0 branch as well. However, since t= he > problem is related to the relative path structures being incorrectly migr= ated > 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 c= hanges > appear to be consolidating some of these issues, but won't be in place un= til > 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 director= y > structure. > Thanks, > ~Sean > > -----Original Message----- > From: ctakes-user-return-31- > Murphy.Sean=3Dmayo.edu@incubator.apache.org [mailto:ctakes-user-return- > 31-Murphy.Sean=3Dmayo.edu@incubator.apache.org] On Behalf Of Chen, Pei > Sent: Thursday, November 15, 2012 3:45 PM > To: > > Cc: >; 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 shou= ld > make the fixes in both trunk and 3.0.0. > > > On Nov 15, 2012, at 10:32 PM, "Murphy, Sean P." > > 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=3Dmayo.edu@incubator.apache.org > > [mailto:ctakes-user-return-29- > Murphy.Sean=3Dmayo.edu@incubator.apache.or > > g] On Behalf Of Chen, Pei > > Sent: Thursday, November 15, 2012 3:15 PM > > To: > > > 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 i= n the > upcoming 3.0 release coming out of ASF as well... Jira#? > > > > > > > > On Nov 15, 2012, at 7:59 PM, "Murphy, Sean P." > > 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 th= e > path structures with the latest cTAKES release. Due to time and resourc= e > constraints we were not able to test each project independently. > >> > >> I will open a bug report against these problems and provide a fix as s= oon > 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=3Dmayo.edu@incubator.apache.org > >> [mailto:ctakes-user-return-26- > Murphy.Sean=3Dmayo.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 sim= ulated > prod smoking tae. So I'll let someone else chime in there. > >> > >> Matt > >> > >> > >> On 2012-11-15 13:11 , "Deepal Dhariwal" > > 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 Mentio= n. > >>> 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 > > 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 > >>>> > >>>> > >> --_000_38DD5510DD255845934ABD523985843B035485MSGPEXCEI11Amfadm_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Thanks Pei,

    &= nbsp;           Agreed.&n= bsp; I believe there was an ant build script built by our team that provide= d an automated means to change the locations when creating the iCTAKES build  from the separate cTAKES projects.   I wasn&= #8217;t sure the nature of the changes to the Maven driven builds, so that&= #8217;s where I misunderstood where and how the changes were to be made.

    &= nbsp;           If okay w= ith everyone I will search all the projects using the old implementation of= the import location relative paths, update and test against 3.0.

    &= nbsp;           Thanks,

    &= nbsp;           &nbs= p;            &= nbsp;  ~Sean

    &= nbsp;          

 <= /p>

From: ctakes-u= ser-return-39-Murphy.Sean=3Dmayo.edu@incubator.apache.org [mailto:ctakes-us= er-return-39-Murphy.Sean=3Dmayo.edu@incubator.apache.org] On Behalf Of Chen, Pei
Sent: Friday, November 30, 2012 12:55 PM
To: ctakes-user@incubator.apache.org; 'Deepal Dhariwal'; 'ctakes-dev= @incubator.apache.org'
Subject: RE: DrugNER & PAD Term Spotter (was: Regarding Assertio= n Tagger)

 

Hi Sean,

It should load the type s= ystem by name instead of path now.

The xml file should:=

<import name=3D"o= rg.apache.ctakes.typesystem.types.TypeSystem"/>

<import name=3D"o= rg.apache.ctakes.drugner.types.TypeSystem"/>

 <= /p>

Instead of:

<import location= =3D"../type_system/NERTypeSyst= em.xml"/>

 <= /p>

While testing this, I als= o noticed that the chunker classname in DrugAggregatePlaintextProcessor.xml= should be:

org.apache.ctakes.chunker= .ae.PhraseTypeChunkCreator

instead of:

edu.mayo.bmi.uima.chunker= .PhraseTypeChunkCreator

 <= /p>

--Pei

 <= /p>

From: Murphy, = Sean P. [mailto:Murphy.Sean@mayo.ed= u]
Sent: Friday, November 30, 2012 1:13 PM
To: 'Deepal Dhariwal'; 'ctakes-dev@incubator.apache.org'
Cc: '<ctakes-= user@incubator.apache.org>'
Subject: RE: Regarding Assertion Tagger

 

I’m able to reprodu= ce the problem on 3.0 in either the prebuild zip bin or the Maven built env= ironment.  The underlying issue appears to be related to the paths not being correctly handled.   I will investigate further.<= /o:p>

 <= /p>

Caused by: org.apache.uim= a.util.InvalidXMLException: Import failed.  Could not read from URL fi= le:/C:/tools/cTAKESv3.0_bin/desc/ctakes-drug-ner/desc/type_system/NERTypeSy= stem.xml. (Descriptor: file:/C:/tools/cTAKESv3.0_bin/desc/ctakes-drug-ner/desc/analy= sis_engine/DrugCNP2LookupWindow.xml)

    &= nbsp;           at org.ap= ache.uima.resource.metadata.impl.TypeSystemDescription_impl.resolveImports(= TypeSystemDescription_impl.java:231)

    &= nbsp;           at org.ap= ache.uima.resource.metadata.impl.TypeSystemDescription_impl.resolveImports(= TypeSystemDescription_impl.java:207)

    &= nbsp;           at org.ap= ache.uima.analysis_engine.metadata.impl.AnalysisEngineMetaData_impl.resolve= Imports(AnalysisEngineMetaData_impl.java:87)

    &= nbsp;           at org.ap= ache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveImport= s(AnalysisEngineDescription_impl.java:741)

    &= nbsp;           at org.ap= ache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelega= teAnalysisEngineImports(AnalysisEngineDescription_impl.java:827)=

    &= nbsp;           at org.ap= ache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveImport= s(AnalysisEngineDescription_impl.java:733)

    &= nbsp;           at org.ap= ache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelega= teAnalysisEngineImports(AnalysisEngineDescription_impl.java:827)=

    &= nbsp;           at org.ap= ache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelega= teAnalysisEngineImports(AnalysisEngineDescription_impl.java:765)=

    &= nbsp;           at org.ap= ache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.getDelegateAn= alysisEngineSpecifiers(AnalysisEngineDescription_impl.java:193)<= /span>

    &= nbsp;           at org.ap= ache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(Aggr= egateAnalysisEngine_impl.java:147)

    &= nbsp;           ... 45 mo= re

Caused by: java.io.FileNo= tFoundException: C:\tools\cTAKESv3.0_bin\desc\ctakes-drug-ner\desc\type_sys= tem\NERTypeSystem.xml (The system cannot find the path specified)

    &= nbsp;           at java.i= o.FileInputStream.open(Native Method)

    &= nbsp;           at java.i= o.FileInputStream.<init>(Unknown Source)

    &= nbsp;           at java.i= o.FileInputStream.<init>(Unknown Source)

    &= nbsp;           at sun.ne= t.www.protocol.file.FileURLConnection.connect(Unknown Source)

    &= nbsp;           at sun.ne= t.www.protocol.file.FileURLConnection.getInputStream(Unknown Source)

    &= nbsp;           at org.ap= ache.uima.util.XMLInputSource.<init>(XMLInputSource.java:120)

    &= nbsp;           at org.ap= ache.uima.resource.metadata.impl.TypeSystemDescription_impl.resolveImport(T= ypeSystemDescription_impl.java:263)

    &= nbsp;           at org.ap= ache.uima.resource.metadata.impl.TypeSystemDescription_impl.resolveImports(= TypeSystemDescription_impl.java:229)

    &= nbsp;           ... 54 mo= re

    &= nbsp;           Thanks,

    &= nbsp;           &nbs= p;            &= nbsp;  ~Sean

 <= /p>

From: Murphy, = Sean P.
Sent: Friday, November 30, 2012 8:58 AM
To: 'Deepal Dhariwal'; ctakes-dev@incubator.apache.org
Cc: <ctakes-u= ser@incubator.apache.org>
Subject: RE: Regarding Assertion Tagger

 

Deepal,=

    &= nbsp;          Thanks for veri= fying #1.   It took a bit longer to setup my environment on a tes= t machine to verify, but please bear with me while I run through a regime of tests regarding these pipelines.    =

 <= /p>

#2. You may need to incre= ase the pool size used by the VM arguments for your java environment. = I believe the default is ” –Xms1024M –Xmx2048M”.&n= bsp;  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.  &nb= sp; Perhaps someone else has some suggestions regarding this aspect(?).

 <= /p>

#3.  I will have to = defer this question to the rest of the team.

 <= /p>

 <= /p>

From: Deepal D= hariwal [mailto:deepaldhariwal@= gmail.com]
Sent: Thursday, November 29, 2012 8:47 PM
To: ctakes-dev@in= cubator.apache.org
Cc: Murphy, Sean P.; <ctakes-user@incubator.apache.org>
Subject: Re: Regarding Assertion Tagger

 

Hello all,

 

1. I downloaded ctakes 3.0 and was trying the PAD te= rm Spotter and Drug NER lookup annotator, but I am getting Resource Initial= ization Exception.I have valid UMLS license and I have added username , pas= sword 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 Col= lection 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 extra= cting cardio vascular terms from medical text using ctakes and umls vocabul= ary. I want to map these terms to existing medical owl ontologies for examp= le, UMLS Semantic Network. I wanted to know whether ctakes community is thinking including medical ontology fe= ature in ctakes.

 

Thanks

Deepal Dhariwal

 

 

On Mon, Nov 26, 2012 at 12:25 PM, Chen, Pei <Pei.Chen@ch= ildrens.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@incu= bator.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 m= igrated
> to the updated format,  I am not sure if the fix should be made t= o the
> sourceforge 2.5 version only or all releases.    The maven d= riven 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 o= n the old directory
> structure.
>       Thanks,
>               ~Sean
>
> -----Original Message-----
> From: ctakes-user-return-31-
> Murphy.Sean=3Dmayo.ed= u@incubator.apache.org [mailto:c= takes-user-return-
> 31-Murphy.Sean=3Dmayo= .edu@incubator.apache.org] On Behalf Of Chen, Pei
> Sent: Thursday, November 15, 2012 3:45 PM
> To: <ctakes-use= r@incubator.apache.org>
> Cc: <ctakes-use= r@incubator.apache.org>; ctakes-dev@incubator.apa= che.org
> Subject: Re: Regarding Assertion Tagger
>
> There's a 3.0.0 branch.  The release will be made from there. &nb= sp;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&g= t; 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=3Dmayo.ed= u@incubator.apache.org
> > [mailto:ctakes-user-ret= urn-29-
> Murphy.S= ean=3Dmayo.edu@incubator.apache.or
> > g] On Behalf Of Chen, Pei
> > Sent: Thursday, November 15, 2012 3:15 PM
> > To: <ctake= s-user@incubator.apache.org>
> > Cc: ctakes-us= er@incubator.apache.org; ctakes-dev@incubator.apa= che.org
> > Subject: Re: Regarding Assertion Tagger
> >
> > Hi Sean,
> > What was the issue in 2.5?  Just want to make sure this is a= lso 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&g= t; 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 re= organization of the
> path structures with the latest cTAKES  release.  Due to tim= e 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 res= olved in a few
> days.
> >>   Thanks,
> >>       ~Sean
> >>
> >> -----Original Message-----
> >> From: ctakes-user-return-26-
> Murphy.Sean=3Dmayo.ed= u@incubator.apache.org
> >> [mailto:ctakes-user= -return-26-
> Murphy.Se= an=3Dmayo.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: ctake= s-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 m= ore
> 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 o= r 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 Ver= sion which
> >>> I have downloaded from
> >>> https://wiki.nci.nih.gov/display/VKC/cTAKES+2.5+User+Install= 3;Instruc
> >>> t
> >>> io
> >>> ns
> >>> .
> >>> I have gone through the cTAKES documentation however no w= here was
> it
> >>> mentioned that polarity / uncertainty properties are on E= ntity Mention.
> >>> In order to avoid sending repeated mails to the mailing l= ist 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 SimulatedProdS= mokingTAE
> >>> Annotator returns smoking status 'unknown' for every inpu= t. 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&#= 43;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 o= n
> >>>> EntityMention and EventMention.
> >>>>
> >>>> Are you using a current development copy of ctakes (f= rom apache svn
> >>>> or from 3.0 RC2)?
> >>>>
> >>>> If not, what version of ctakes are you using?  V= ersion number?
> >>>> Binary, source zip, or source from svn?
> >>>>
> >>>> Matt
> >>>>
> >>>>
> >>

 

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