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Posted to dev@ctakes.apache.org by Deepal Dhariwal <de...@gmail.com> on 2012/11/14 21:07:14 UTC
Fwd: Regarding Assertion Tagger
---------- Forwarded message ----------
From: Deepal Dhariwal <de...@gmail.com>
Date: Wed, Nov 14, 2012 at 8:37 AM
Subject: Regarding Assertion Tagger
To: ctakes-users@incubator.apache.org
Hello
I want to assert presence of medical terms using cTAKESdesc \ assertiondesc
\ AssertionAnalysisEngine. However when I load and execute this analysis
engine using cTakes CVD I am getting the following exception.
org.apache.uima.analysis_engine.AnalysisEngineProcessException: Anootator
processing failed. More detailed information is in the log file.
Kindly let me know the cause of exception and the location where log files
are generated.
Thanks
Deepal Dhariwal
RE: Regarding Assertion Tagger
Posted by "Masanz, James J." <Ma...@mayo.edu>.
Hi Deepal,
If by question #3, you are looking for a way to get a mapping from a cTAKES annotation to the semantic type for the concept, this is already done within cTAKES (for the following 4 groupings: Diseases/disorders, Signs/symptoms, Procedures, Anatomical sites)
FYI, These groupings are based on the lists of TUIs within the LookupDesc*.xml files within cTAKES.
The concept (aka clinical named entity) annotations created by cTAKES are linked to UmlsConcept annotations, which contain an attribute called tui.
>From the TUI (such as T047) you can map to the textual name of the semantic type such as "Disease or Syndrome"
See the annotations of type UmlsConcept that are produced by cTAKES, which include the CUI and the TUI, and you can map to the list of semantic type names from this table:
http://semanticnetwork.nlm.nih.gov/Download/RelationalFiles/SRDEF
For example, if cTAKES annotates "AIDS", there will be a UmlsConcept annotation with cui="C0011884" tui="T047", where T047 is the TUI for "Disease or Syndrome"
Regards,
James Masanz
From: ctakes-user-return-37-Masanz.James=mayo.edu@incubator.apache.org [mailto:ctakes-user-return-37-Masanz.James=mayo.edu@incubator.apache.org] On Behalf Of Murphy, Sean P.
Sent: Friday, November 30, 2012 8:58 AM
To: 'Deepal Dhariwal'; ctakes-dev@incubator.apache.org
Cc: <ct...@incubator.apache.org>
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 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:deepaldhariwal@gmail.com]
Sent: Thursday, November 29, 2012 8:47 PM
To: ctakes-dev@incubator.apache.org
Cc: Murphy, Sean P.; <ct...@incubator.apache.org>
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 <Pe...@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; <ct...@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: <ct...@incubator.apache.org>
> Cc: <ct...@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."
> <Mu...@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: <ct...@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."
> <Mu...@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" <de...@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 <mc...@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
> >>>>
> >>>>
> >>
RE: Regarding Assertion Tagger
Posted by "Murphy, Sean P." <Mu...@mayo.edu>.
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/type_system/NERTypeSystem.xml. (Descriptor: file:/C:/tools/cTAKESv3.0_bin/desc/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml)
at org.apache.uima.resource.metadata.impl.TypeSystemDescription_impl.resolveImports(TypeSystemDescription_impl.java:231)
at org.apache.uima.resource.metadata.impl.TypeSystemDescription_impl.resolveImports(TypeSystemDescription_impl.java:207)
at org.apache.uima.analysis_engine.metadata.impl.AnalysisEngineMetaData_impl.resolveImports(AnalysisEngineMetaData_impl.java:87)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveImports(AnalysisEngineDescription_impl.java:741)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:827)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveImports(AnalysisEngineDescription_impl.java:733)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:827)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:765)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.getDelegateAnalysisEngineSpecifiers(AnalysisEngineDescription_impl.java:193)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:147)
... 45 more
Caused by: java.io.FileNotFoundException: C:\tools\cTAKESv3.0_bin\desc\ctakes-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.<init>(Unknown Source)
at java.io.FileInputStream.<init>(Unknown Source)
at sun.net.www.protocol.file.FileURLConnection.connect(Unknown Source)
at sun.net.www.protocol.file.FileURLConnection.getInputStream(Unknown Source)
at org.apache.uima.util.XMLInputSource.<init>(XMLInputSource.java:120)
at org.apache.uima.resource.metadata.impl.TypeSystemDescription_impl.resolveImport(TypeSystemDescription_impl.java:263)
at org.apache.uima.resource.metadata.impl.TypeSystemDescription_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: <ct...@incubator.apache.org>
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 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:deepaldhariwal@gmail.com]
Sent: Thursday, November 29, 2012 8:47 PM
To: ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>
Cc: Murphy, Sean P.; <ct...@incubator.apache.org>>
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 <Pe...@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<ma...@mayo.edu>]
> Sent: Monday, November 26, 2012 12:21 PM
> To: Chen, Pei
> Cc: ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>; <ct...@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<ma...@incubator.apache.org> [mailto:ctakes-user-return-<mailto:ctakes-user-return->
> 31-Murphy.Sean=mayo.edu@incubator.apache.org<ma...@incubator.apache.org>] On Behalf Of Chen, Pei
> Sent: Thursday, November 15, 2012 3:45 PM
> To: <ct...@incubator.apache.org>>
> Cc: <ct...@incubator.apache.org>>; ctakes-dev@incubator.apache.org<ma...@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."
> <Mu...@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<ma...@incubator.apache.org>
> > [mailto:ctakes-user-return-29-<mailto:ctakes-user-return-29->
> Murphy.Sean=mayo.edu@incubator.apache.or<ma...@incubator.apache.or>
> > g] On Behalf Of Chen, Pei
> > Sent: Thursday, November 15, 2012 3:15 PM
> > To: <ct...@incubator.apache.org>>
> > Cc: ctakes-user@incubator.apache.org<ma...@incubator.apache.org>; ctakes-dev@incubator.apache.org<ma...@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."
> <Mu...@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<ma...@incubator.apache.org>
> >> [mailto:ctakes-user-return-26-<mailto:ctakes-user-return-26->
> Murphy.Sean=mayo.edu@incubator.apache.o<ma...@incubator.apache.o>
> >> r
> >> g] On Behalf Of Coarr, Matt
> >> Sent: Thursday, November 15, 2012 12:22 PM
> >> To: ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>
> >> Cc: ctakes-user@incubator.apache.org<ma...@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" <de...@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 <mc...@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
> >>>>
> >>>>
> >>
RE: Regarding Assertion Tagger
Posted by "Murphy, Sean P." <Mu...@mayo.edu>.
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/type_system/NERTypeSystem.xml. (Descriptor: file:/C:/tools/cTAKESv3.0_bin/desc/ctakes-drug-ner/desc/analysis_engine/DrugCNP2LookupWindow.xml)
at org.apache.uima.resource.metadata.impl.TypeSystemDescription_impl.resolveImports(TypeSystemDescription_impl.java:231)
at org.apache.uima.resource.metadata.impl.TypeSystemDescription_impl.resolveImports(TypeSystemDescription_impl.java:207)
at org.apache.uima.analysis_engine.metadata.impl.AnalysisEngineMetaData_impl.resolveImports(AnalysisEngineMetaData_impl.java:87)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveImports(AnalysisEngineDescription_impl.java:741)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:827)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveImports(AnalysisEngineDescription_impl.java:733)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:827)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.resolveDelegateAnalysisEngineImports(AnalysisEngineDescription_impl.java:765)
at org.apache.uima.analysis_engine.impl.AnalysisEngineDescription_impl.getDelegateAnalysisEngineSpecifiers(AnalysisEngineDescription_impl.java:193)
at org.apache.uima.analysis_engine.impl.AggregateAnalysisEngine_impl.initialize(AggregateAnalysisEngine_impl.java:147)
... 45 more
Caused by: java.io.FileNotFoundException: C:\tools\cTAKESv3.0_bin\desc\ctakes-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.<init>(Unknown Source)
at java.io.FileInputStream.<init>(Unknown Source)
at sun.net.www.protocol.file.FileURLConnection.connect(Unknown Source)
at sun.net.www.protocol.file.FileURLConnection.getInputStream(Unknown Source)
at org.apache.uima.util.XMLInputSource.<init>(XMLInputSource.java:120)
at org.apache.uima.resource.metadata.impl.TypeSystemDescription_impl.resolveImport(TypeSystemDescription_impl.java:263)
at org.apache.uima.resource.metadata.impl.TypeSystemDescription_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: <ct...@incubator.apache.org>
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 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:deepaldhariwal@gmail.com]
Sent: Thursday, November 29, 2012 8:47 PM
To: ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>
Cc: Murphy, Sean P.; <ct...@incubator.apache.org>>
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 <Pe...@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<ma...@mayo.edu>]
> Sent: Monday, November 26, 2012 12:21 PM
> To: Chen, Pei
> Cc: ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>; <ct...@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<ma...@incubator.apache.org> [mailto:ctakes-user-return-<mailto:ctakes-user-return->
> 31-Murphy.Sean=mayo.edu@incubator.apache.org<ma...@incubator.apache.org>] On Behalf Of Chen, Pei
> Sent: Thursday, November 15, 2012 3:45 PM
> To: <ct...@incubator.apache.org>>
> Cc: <ct...@incubator.apache.org>>; ctakes-dev@incubator.apache.org<ma...@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."
> <Mu...@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<ma...@incubator.apache.org>
> > [mailto:ctakes-user-return-29-<mailto:ctakes-user-return-29->
> Murphy.Sean=mayo.edu@incubator.apache.or<ma...@incubator.apache.or>
> > g] On Behalf Of Chen, Pei
> > Sent: Thursday, November 15, 2012 3:15 PM
> > To: <ct...@incubator.apache.org>>
> > Cc: ctakes-user@incubator.apache.org<ma...@incubator.apache.org>; ctakes-dev@incubator.apache.org<ma...@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."
> <Mu...@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<ma...@incubator.apache.org>
> >> [mailto:ctakes-user-return-26-<mailto:ctakes-user-return-26->
> Murphy.Sean=mayo.edu@incubator.apache.o<ma...@incubator.apache.o>
> >> r
> >> g] On Behalf Of Coarr, Matt
> >> Sent: Thursday, November 15, 2012 12:22 PM
> >> To: ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>
> >> Cc: ctakes-user@incubator.apache.org<ma...@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" <de...@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 <mc...@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
> >>>>
> >>>>
> >>
RE: Regarding Assertion Tagger
Posted by "Murphy, Sean P." <Mu...@mayo.edu>.
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:deepaldhariwal@gmail.com]
Sent: Thursday, November 29, 2012 8:47 PM
To: ctakes-dev@incubator.apache.org
Cc: Murphy, Sean P.; <ct...@incubator.apache.org>
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 <Pe...@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<ma...@mayo.edu>]
> Sent: Monday, November 26, 2012 12:21 PM
> To: Chen, Pei
> Cc: ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>; <ct...@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<ma...@incubator.apache.org> [mailto:ctakes-user-return-<mailto:ctakes-user-return->
> 31-Murphy.Sean=mayo.edu@incubator.apache.org<ma...@incubator.apache.org>] On Behalf Of Chen, Pei
> Sent: Thursday, November 15, 2012 3:45 PM
> To: <ct...@incubator.apache.org>>
> Cc: <ct...@incubator.apache.org>>; ctakes-dev@incubator.apache.org<ma...@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."
> <Mu...@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<ma...@incubator.apache.org>
> > [mailto:ctakes-user-return-29-<mailto:ctakes-user-return-29->
> Murphy.Sean=mayo.edu@incubator.apache.or<ma...@incubator.apache.or>
> > g] On Behalf Of Chen, Pei
> > Sent: Thursday, November 15, 2012 3:15 PM
> > To: <ct...@incubator.apache.org>>
> > Cc: ctakes-user@incubator.apache.org<ma...@incubator.apache.org>; ctakes-dev@incubator.apache.org<ma...@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."
> <Mu...@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<ma...@incubator.apache.org>
> >> [mailto:ctakes-user-return-26-<mailto:ctakes-user-return-26->
> Murphy.Sean=mayo.edu@incubator.apache.o<ma...@incubator.apache.o>
> >> r
> >> g] On Behalf Of Coarr, Matt
> >> Sent: Thursday, November 15, 2012 12:22 PM
> >> To: ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>
> >> Cc: ctakes-user@incubator.apache.org<ma...@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" <de...@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 <mc...@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
> >>>>
> >>>>
> >>
RE: Regarding Assertion Tagger
Posted by "Murphy, Sean P." <Mu...@mayo.edu>.
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:deepaldhariwal@gmail.com]
Sent: Thursday, November 29, 2012 8:47 PM
To: ctakes-dev@incubator.apache.org
Cc: Murphy, Sean P.; <ct...@incubator.apache.org>
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 <Pe...@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<ma...@mayo.edu>]
> Sent: Monday, November 26, 2012 12:21 PM
> To: Chen, Pei
> Cc: ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>; <ct...@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<ma...@incubator.apache.org> [mailto:ctakes-user-return-<mailto:ctakes-user-return->
> 31-Murphy.Sean=mayo.edu@incubator.apache.org<ma...@incubator.apache.org>] On Behalf Of Chen, Pei
> Sent: Thursday, November 15, 2012 3:45 PM
> To: <ct...@incubator.apache.org>>
> Cc: <ct...@incubator.apache.org>>; ctakes-dev@incubator.apache.org<ma...@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."
> <Mu...@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<ma...@incubator.apache.org>
> > [mailto:ctakes-user-return-29-<mailto:ctakes-user-return-29->
> Murphy.Sean=mayo.edu@incubator.apache.or<ma...@incubator.apache.or>
> > g] On Behalf Of Chen, Pei
> > Sent: Thursday, November 15, 2012 3:15 PM
> > To: <ct...@incubator.apache.org>>
> > Cc: ctakes-user@incubator.apache.org<ma...@incubator.apache.org>; ctakes-dev@incubator.apache.org<ma...@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."
> <Mu...@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<ma...@incubator.apache.org>
> >> [mailto:ctakes-user-return-26-<mailto:ctakes-user-return-26->
> Murphy.Sean=mayo.edu@incubator.apache.o<ma...@incubator.apache.o>
> >> r
> >> g] On Behalf Of Coarr, Matt
> >> Sent: Thursday, November 15, 2012 12:22 PM
> >> To: ctakes-dev@incubator.apache.org<ma...@incubator.apache.org>
> >> Cc: ctakes-user@incubator.apache.org<ma...@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" <de...@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 <mc...@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
> >>>>
> >>>>
> >>
Re: Regarding Assertion Tagger
Posted by Deepal Dhariwal <de...@gmail.com>.
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
<Pe...@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; <ct...@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: <ct...@incubator.apache.org>
> > Cc: <ct...@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."
> > <Mu...@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: <ct...@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."
> > <Mu...@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" <de...@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 <mc...@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
> > >>>>
> > >>>>
> > >>
>
Re: Regarding Assertion Tagger
Posted by Deepal Dhariwal <de...@gmail.com>.
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
<Pe...@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; <ct...@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: <ct...@incubator.apache.org>
> > Cc: <ct...@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."
> > <Mu...@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: <ct...@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."
> > <Mu...@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" <de...@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 <mc...@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
> > >>>>
> > >>>>
> > >>
>
RE: Regarding Assertion Tagger
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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; <ct...@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: <ct...@incubator.apache.org>
> Cc: <ct...@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."
> <Mu...@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: <ct...@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."
> <Mu...@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" <de...@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 <mc...@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
> >>>>
> >>>>
> >>
RE: Regarding Assertion Tagger
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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; <ct...@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: <ct...@incubator.apache.org>
> Cc: <ct...@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."
> <Mu...@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: <ct...@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."
> <Mu...@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" <de...@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 <mc...@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
> >>>>
> >>>>
> >>
RE: Regarding Assertion Tagger
Posted by "Murphy, Sean P." <Mu...@mayo.edu>.
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: <ct...@incubator.apache.org>
Cc: <ct...@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." <Mu...@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: <ct...@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." <Mu...@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" <de...@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 <mc...@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
>>>>
>>>>
>>
RE: Regarding Assertion Tagger
Posted by "Murphy, Sean P." <Mu...@mayo.edu>.
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: <ct...@incubator.apache.org>
Cc: <ct...@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." <Mu...@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: <ct...@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." <Mu...@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" <de...@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 <mc...@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
>>>>
>>>>
>>
Re: Regarding Assertion Tagger
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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." <Mu...@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.org] On Behalf Of Chen, Pei
> Sent: Thursday, November 15, 2012 3:15 PM
> To: <ct...@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." <Mu...@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.or
>> 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" <de...@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+Instruct
>>> 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 <mc...@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
>>>>
>>>>
>>
Re: Regarding Assertion Tagger
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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." <Mu...@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.org] On Behalf Of Chen, Pei
> Sent: Thursday, November 15, 2012 3:15 PM
> To: <ct...@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." <Mu...@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.or
>> 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" <de...@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+Instruct
>>> 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 <mc...@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
>>>>
>>>>
>>
RE: Regarding Assertion Tagger
Posted by "Murphy, Sean P." <Mu...@mayo.edu>.
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.org] On Behalf Of Chen, Pei
Sent: Thursday, November 15, 2012 3:15 PM
To: <ct...@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." <Mu...@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.or
> 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" <de...@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+Instruct
>> 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 <mc...@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
>>>
>>>
>
RE: Regarding Assertion Tagger
Posted by "Murphy, Sean P." <Mu...@mayo.edu>.
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.org] On Behalf Of Chen, Pei
Sent: Thursday, November 15, 2012 3:15 PM
To: <ct...@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." <Mu...@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.or
> 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" <de...@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+Instruct
>> 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 <mc...@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
>>>
>>>
>
Re: Regarding Assertion Tagger
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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." <Mu...@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.org] 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" <de...@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+Instructio
>> 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 <mc...@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
>>>
>>>
>
Re: Regarding Assertion Tagger
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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." <Mu...@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.org] 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" <de...@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+Instructio
>> 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 <mc...@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
>>>
>>>
>
RE: Regarding Assertion Tagger
Posted by "Murphy, Sean P." <Mu...@mayo.edu>.
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.org] 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" <de...@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+Instructio
>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 <mc...@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
>>
>>
RE: Regarding Assertion Tagger
Posted by "Murphy, Sean P." <Mu...@mayo.edu>.
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.org] 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" <de...@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+Instructio
>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 <mc...@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
>>
>>
Re: Regarding Assertion Tagger
Posted by "Coarr, Matt" <mc...@mitre.org>.
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" <de...@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+Instructions
>.
> 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 <mc...@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
>>
>>
Re: Regarding Assertion Tagger
Posted by "Coarr, Matt" <mc...@mitre.org>.
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" <de...@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+Instructions
>.
> 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 <mc...@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
>>
>>
Re: Regarding Assertion Tagger
Posted by Deepal Dhariwal <de...@gmail.com>.
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+Instructions .
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 <mc...@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
>
>
Re: Regarding Assertion Tagger
Posted by Deepal Dhariwal <de...@gmail.com>.
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+Instructions .
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 <mc...@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
>
>
Re: Regarding Assertion Tagger
Posted by "Coarr, Matt" <mc...@mitre.org>.
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
Re: Regarding Assertion Tagger
Posted by "Coarr, Matt" <mc...@mitre.org>.
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
Re: Regarding Assertion Tagger
Posted by Deepal Dhariwal <de...@gmail.com>.
Hello Matt,
Thanks for your reply. So currently my concept annotation produces
properties are begin, end, concept type, concept Text, externalId,
originalexternalID. However the annotation does not include polarity /
conditional / uncertain. So shall I use Collection Processing Engine with
AggregatePlainTextProcessor followed by AssertionMiniPipeLineAnalysis ?
Further I am also trying Peripheral Artery Disease Spotter. However even
that annotator returns only Document Annotation.
Thanks
Deepal Dhariwal
On Thu, Nov 15, 2012 at 9:35 AM, Coarr, Matt <mc...@mitre.org> wrote:
> Hi Deepal,
>
> The Concept annotation is an internal temporary annotation used by the
> assertion module (created based on the combination of the entity mention
> and ontology concepts).
>
> The assertion module does not produce new annotations. Instead it sets
> properties on the existing entity mention annotations (the properties are
> polarity, conditional, and uncertainty).
>
> Matt
>
>
> On 2012-11-15 07:44 , "Deepal Dhariwal" <de...@gmail.com> wrote:
>
> >Hello Chen,
> >
> >Thanks for your reply. I tried AggregatePlainTextUMLSProcessor Analysis
> >Engine from cdpdesc. However it does not return assertion for presence of
> >medical concept. The org.mitre.medfacts.type.Concept returns begin, end
> >of
> >span, concept Type, concept Text and not whether the concept is
> >conditionally present or absent.
> >Thanks for log file. It is found in Tools -> View Log file.
> >
> >Regards
> >Deepal Dhariwal
> >
> >On Wed, Nov 14, 2012 at 4:59 PM, Chen, Pei
> ><Pe...@childrens.harvard.edu>wrote:
> >
> >> Fyi
> >> Also feel free to subscribe to the dev group.
> >>
> >> -----Original Message-----
> >> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> >> Sent: Wednesday, November 14, 2012 3:20 PM
> >> To: <ct...@incubator.apache.org>
> >> Cc: ctakes-users@incubator.apache.org; ctakes-dev@incubator.apache.org
> >> Subject: Re: Regarding Assertion Tagger
> >>
> >> Hi Deepal,
> >> I presume you are using v2.5.
> >> Did you know that the DefaultAggregatePipeline.xml from the cdp(clinical
> >> documents pipeline) folder should already have the negation/assertion
> >> module included for the identified annotations?
> >>
> >> Re:log in the CVD. There should be a menu option in the UIMA CVD
> >>view>log
> >> file.
> >> I hope that helps.
> >>
> >> Sent from my iPhone
> >>
> >> On Nov 14, 2012, at 9:09 PM, "Deepal Dhariwal"
> >><de...@gmail.com>
> >> wrote:
> >>
> >> > ---------- Forwarded message ----------
> >> > From: Deepal Dhariwal <de...@gmail.com>
> >> > Date: Wed, Nov 14, 2012 at 8:37 AM
> >> > Subject: Regarding Assertion Tagger
> >> > To: ctakes-users@incubator.apache.org
> >> >
> >> >
> >> > Hello
> >> > I want to assert presence of medical terms using cTAKESdesc \
> >> > assertiondesc \ AssertionAnalysisEngine. However when I load and
> >> > execute this analysis engine using cTakes CVD I am getting the
> >>following
> >> exception.
> >> > org.apache.uima.analysis_engine.AnalysisEngineProcessException:
> >> > Anootator processing failed. More detailed information is in the log
> >> file.
> >> >
> >> > Kindly let me know the cause of exception and the location where log
> >> > files are generated.
> >> >
> >> > Thanks
> >> > Deepal Dhariwal
> >>
>
>
Re: Regarding Assertion Tagger
Posted by "Coarr, Matt" <mc...@mitre.org>.
Hi Deepal,
The Concept annotation is an internal temporary annotation used by the
assertion module (created based on the combination of the entity mention
and ontology concepts).
The assertion module does not produce new annotations. Instead it sets
properties on the existing entity mention annotations (the properties are
polarity, conditional, and uncertainty).
Matt
On 2012-11-15 07:44 , "Deepal Dhariwal" <de...@gmail.com> wrote:
>Hello Chen,
>
>Thanks for your reply. I tried AggregatePlainTextUMLSProcessor Analysis
>Engine from cdpdesc. However it does not return assertion for presence of
>medical concept. The org.mitre.medfacts.type.Concept returns begin, end
>of
>span, concept Type, concept Text and not whether the concept is
>conditionally present or absent.
>Thanks for log file. It is found in Tools -> View Log file.
>
>Regards
>Deepal Dhariwal
>
>On Wed, Nov 14, 2012 at 4:59 PM, Chen, Pei
><Pe...@childrens.harvard.edu>wrote:
>
>> Fyi
>> Also feel free to subscribe to the dev group.
>>
>> -----Original Message-----
>> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
>> Sent: Wednesday, November 14, 2012 3:20 PM
>> To: <ct...@incubator.apache.org>
>> Cc: ctakes-users@incubator.apache.org; ctakes-dev@incubator.apache.org
>> Subject: Re: Regarding Assertion Tagger
>>
>> Hi Deepal,
>> I presume you are using v2.5.
>> Did you know that the DefaultAggregatePipeline.xml from the cdp(clinical
>> documents pipeline) folder should already have the negation/assertion
>> module included for the identified annotations?
>>
>> Re:log in the CVD. There should be a menu option in the UIMA CVD
>>view>log
>> file.
>> I hope that helps.
>>
>> Sent from my iPhone
>>
>> On Nov 14, 2012, at 9:09 PM, "Deepal Dhariwal"
>><de...@gmail.com>
>> wrote:
>>
>> > ---------- Forwarded message ----------
>> > From: Deepal Dhariwal <de...@gmail.com>
>> > Date: Wed, Nov 14, 2012 at 8:37 AM
>> > Subject: Regarding Assertion Tagger
>> > To: ctakes-users@incubator.apache.org
>> >
>> >
>> > Hello
>> > I want to assert presence of medical terms using cTAKESdesc \
>> > assertiondesc \ AssertionAnalysisEngine. However when I load and
>> > execute this analysis engine using cTakes CVD I am getting the
>>following
>> exception.
>> > org.apache.uima.analysis_engine.AnalysisEngineProcessException:
>> > Anootator processing failed. More detailed information is in the log
>> file.
>> >
>> > Kindly let me know the cause of exception and the location where log
>> > files are generated.
>> >
>> > Thanks
>> > Deepal Dhariwal
>>
Re: FW: Regarding Assertion Tagger
Posted by Deepal Dhariwal <de...@gmail.com>.
Hello Chen,
Thanks for your reply. I tried AggregatePlainTextUMLSProcessor Analysis
Engine from cdpdesc. However it does not return assertion for presence of
medical concept. The org.mitre.medfacts.type.Concept returns begin, end of
span, concept Type, concept Text and not whether the concept is
conditionally present or absent.
Thanks for log file. It is found in Tools -> View Log file.
Regards
Deepal Dhariwal
On Wed, Nov 14, 2012 at 4:59 PM, Chen, Pei
<Pe...@childrens.harvard.edu>wrote:
> Fyi
> Also feel free to subscribe to the dev group.
>
> -----Original Message-----
> From: Chen, Pei [mailto:Pei.Chen@childrens.harvard.edu]
> Sent: Wednesday, November 14, 2012 3:20 PM
> To: <ct...@incubator.apache.org>
> Cc: ctakes-users@incubator.apache.org; ctakes-dev@incubator.apache.org
> Subject: Re: Regarding Assertion Tagger
>
> Hi Deepal,
> I presume you are using v2.5.
> Did you know that the DefaultAggregatePipeline.xml from the cdp(clinical
> documents pipeline) folder should already have the negation/assertion
> module included for the identified annotations?
>
> Re:log in the CVD. There should be a menu option in the UIMA CVD view>log
> file.
> I hope that helps.
>
> Sent from my iPhone
>
> On Nov 14, 2012, at 9:09 PM, "Deepal Dhariwal" <de...@gmail.com>
> wrote:
>
> > ---------- Forwarded message ----------
> > From: Deepal Dhariwal <de...@gmail.com>
> > Date: Wed, Nov 14, 2012 at 8:37 AM
> > Subject: Regarding Assertion Tagger
> > To: ctakes-users@incubator.apache.org
> >
> >
> > Hello
> > I want to assert presence of medical terms using cTAKESdesc \
> > assertiondesc \ AssertionAnalysisEngine. However when I load and
> > execute this analysis engine using cTakes CVD I am getting the following
> exception.
> > org.apache.uima.analysis_engine.AnalysisEngineProcessException:
> > Anootator processing failed. More detailed information is in the log
> file.
> >
> > Kindly let me know the cause of exception and the location where log
> > files are generated.
> >
> > Thanks
> > Deepal Dhariwal
>
Re: Regarding Assertion Tagger
Posted by "Coarr, Matt" <mc...@mitre.org>.
The assertion module cannot be run on its own, it depends on other
annotations.
It's typically requires running in the clinical document pipeline that Pei
mentioned.
If you really want to run it by itself, you'll have to provide sentence,
token (and it's subclasses), and entities (and their associated ontology
concepts).
Even in this case, you should still run
AssertionMiniPipelineAnalysisEngine.xml (instead of
assertionAnalysisEngine.xml). This calls conceptConverterAnysisEngine.xml
before assertionAnalysisEngine.xml.
Matt
On 2012-11-14 15:18 , "Chen, Pei" <Pe...@childrens.harvard.edu> wrote:
>Hi Deepal,
>I presume you are using v2.5.
>Did you know that the DefaultAggregatePipeline.xml from the cdp(clinical
>documents pipeline) folder should already have the negation/assertion
>module included for the identified annotations?
>
>Re:log in the CVD. There should be a menu option in the UIMA CVD view>log
>file.
>I hope that helps.
>
>Sent from my iPhone
>
>On Nov 14, 2012, at 9:09 PM, "Deepal Dhariwal" <de...@gmail.com>
>wrote:
>
>> ---------- Forwarded message ----------
>> From: Deepal Dhariwal <de...@gmail.com>
>> Date: Wed, Nov 14, 2012 at 8:37 AM
>> Subject: Regarding Assertion Tagger
>> To: ctakes-users@incubator.apache.org
>>
>>
>> Hello
>> I want to assert presence of medical terms using cTAKESdesc \
>>assertiondesc
>> \ AssertionAnalysisEngine. However when I load and execute this analysis
>> engine using cTakes CVD I am getting the following exception.
>> org.apache.uima.analysis_engine.AnalysisEngineProcessException:
>>Anootator
>> processing failed. More detailed information is in the log file.
>>
>> Kindly let me know the cause of exception and the location where log
>>files
>> are generated.
>>
>> Thanks
>> Deepal Dhariwal
Re: Regarding Assertion Tagger
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
Hi Deepal,
I presume you are using v2.5.
Did you know that the DefaultAggregatePipeline.xml from the cdp(clinical documents pipeline) folder should already have the negation/assertion module included for the identified annotations?
Re:log in the CVD. There should be a menu option in the UIMA CVD view>log file.
I hope that helps.
Sent from my iPhone
On Nov 14, 2012, at 9:09 PM, "Deepal Dhariwal" <de...@gmail.com> wrote:
> ---------- Forwarded message ----------
> From: Deepal Dhariwal <de...@gmail.com>
> Date: Wed, Nov 14, 2012 at 8:37 AM
> Subject: Regarding Assertion Tagger
> To: ctakes-users@incubator.apache.org
>
>
> Hello
> I want to assert presence of medical terms using cTAKESdesc \ assertiondesc
> \ AssertionAnalysisEngine. However when I load and execute this analysis
> engine using cTakes CVD I am getting the following exception.
> org.apache.uima.analysis_engine.AnalysisEngineProcessException: Anootator
> processing failed. More detailed information is in the log file.
>
> Kindly let me know the cause of exception and the location where log files
> are generated.
>
> Thanks
> Deepal Dhariwal