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Posted to dev@ctakes.apache.org by Sourabh Mukherjee <so...@gmail.com> on 2017/09/08 08:16:45 UTC
ctakes timelanes
Hi,
I followed the steps mentioned in the link "
http://mail-archives.apache.org/mod_mbox/ctakes-dev/201603.mbox/%3CF968C6DCE9D2F04CB8519CB3ACF06E99B83311B8@ex04.net.ucsf.edu%3E"
and without any error. I am feeding the input as the xmi file ,tried with
simple txt files too but couldn't see and timelines or any data at all. It
is just that the UI is popping up , taking the input file but showing no
output. Am I missing something, can somebody help me to understand why
there is no output. Thanks in advance for the help.
Regards,
Sourabh
RE: ctakes timelanes [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Oh yeah - I should have mentioned that ... I immediately focused upon the stack trace.
Thanks Tim!
I just checked in a TemporalSubPipe.piper file. So if you are using a piper you can just add the line:
load TemporalSubPipe.piper
In case you want to use annotators selectively, the piper commands are:
// 'Generic' Events. Use addDescription and let the EventAnnotator set itself up with defaults.
addDescription EventAnnotator
// Times. Use addLogged to log start and finish of processing. There aren't default models, so set specifically
addLogged BackwardsTimeAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/timeannotator/model.jar
// DocTimeRel: the relation bin for Events to the Document Creation Time.
addLogged DocTimeRelAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/doctimerel/model.jar
// Event - Time binary relations.
addLogged EventTimeRelationAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/eventtime/model.jar
// Event - Event binary relations.
addLogged EventEventRelationAnnotator classifierJarPath=/org/apache/ctakes/temporal/ae/eventevent/model.jar
Sean
-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
Sent: Friday, September 15, 2017 9:08 AM
To: dev@ctakes.apache.org
Subject: Re: ctakes timelanes [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]
Sourabh, that is not the right way to run the temporal pipelines. That class is one we use for running evaluations on standard datasets for writing papers. You need to add the temporal components to the end of your existing pipeline (before the xmi writer part). Here is an example of how it's done using uimafit:
https://urldefense.proofpoint.com/v2/url?u=http-3A__svn.apache.org_viewvc_ctakes_tags_ctakes-2D4.0.0_ctakes-2Dtemporal_src_main_java_org_apache_ctakes_temporal_pipelines_FullTemporalExtractionPipeline.java-3Fview-3Dmarkup&d=DwIFAw&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=9sUikseCzqZ01uVxjexTfAX56q4dLE7vNjg80Y53n0Q&s=aYUKi6GWs9O4icmRi04-a1AvIFuF_NfI1lvDet5WJbY&e=
if you are using piper files or uima xml descriptors you will need to adapt these.
Tim
________________________________________
From: Finan, Sean <Se...@childrens.harvard.edu>
Sent: Friday, September 15, 2017 9:03 AM
To: dev@ctakes.apache.org
Subject: RE: ctakes timelanes [EXTERNAL] [SUSPICIOUS]
Hi Sourabh,
Does the run stop? I occasionally see that same error in another pipeline but it doesn't stop the run.
Thanks,
Sean
-----Original Message-----
From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
Sent: Friday, September 15, 2017 1:47 AM
To: Apache cTAKES Dev
Subject: Re: ctakes timelanes [EXTERNAL]
Thanks Sean. If my understanding is correct Timelanes expect an XMI input having temoral and entity information. Hence I am using ctakes temporal package to extract the info. I tried executing EvaluationOfEventTimeRelations.java with the following parameters
"--text=E:/cTakes/apache-ctakes-4.0.0/bin/testdata/input/ --format=Anafora --xml=F:/sourabhmukherjee/thymedata-master/coloncancer/Test/ID006_clinic_016/
--xmi=E:/cTakes/apache-ctakes-4.0.0/bin/testdata/ouput --kernelParams="c
0.001953125 t 0.03125 d 3 g 1.0 S 1 C + L 0.5 T 0.1 N 3" --patients=1-218 --useGoldAttributes"
But I am getting the following error when tried to run it in eclipse
Error with parameter settings:
,Kernel=tk,Cost=10.0,Gamma=1.0,secondKernel=polynomial,operator=SUM,tkWeight=0.1,lambda=0.1
org.apache.uima.resource.ResourceInitializationException: The feature org.apache.ctakes.typesystem.type.textspan.List:items is declared twice, with incompatible multipleReferencesAllowed specifications. (Descriptor:
jar:file:/E:/cTakes/apache-ctakes-4.0.0/lib/ctakes-type-system-4.0.0.jar!/org/apache/ctakes/typesystem/types/TypeSystem.xml)
at
org.apache.uima.util.CasCreationUtils.mergeFeatures(CasCreationUtils.java:1709)
at
org.apache.uima.util.CasCreationUtils.addTypeToMergedTypeSystem(CasCreationUtils.java:1178)
at
org.apache.uima.util.CasCreationUtils.mergeTypeSystems(CasCreationUtils.java:1100)
at
org.apache.uima.util.CasCreationUtils.mergeTypeSystems(CasCreationUtils.java:1029)
at
org.apache.uima.fit.factory.TypeSystemDescriptionFactory.createTypeSystemDescription(TypeSystemDescriptionFactory.java:119)
at
org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineDescription(AnalysisEngineFactory.java:978)
at
org.cleartk.util.ae.UriToDocumentTextAnnotator.getDescription(UriToDocumentTextAnnotator.java:58)
at
org.apache.ctakes.temporal.eval.Evaluation_ImplBase.getXMIReadingPreprocessorAggregateBuilder(Evaluation_ImplBase.java:471)
at
org.apache.ctakes.temporal.eval.Evaluation_ImplBase.getPreprocessorAggregateBuilder(Evaluation_ImplBase.java:464)
at
org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.train(EvaluationOfEventTimeRelations.java:303)
at
org.cleartk.eval.Evaluation_ImplBase.trainAndTest(Evaluation_ImplBase.java:76)
at
org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.main(EvaluationOfEventTimeRelations.java:211)
It would be a great help if somebody helps me here since I am new to both ctakes and Java.
Thanks in advance for your help.
Regards,
Sourabh
On Wed, Sep 13, 2017 at 9:10 AM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:
> Hi Sourabh,
>
> The timelanes gui displays temporal information extracted by ctakes on
> a timeline. That information is extracted by the ctakes-temporal module.
> Without temporal information it can still display a markup of the text
> and allow searching, etc. but is no more useful than many other
> annotation markup tools.
>
> You can find the wiki page for the temporal module here:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_
> confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS
> dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=CmDrS1CLFg
> yz2OkgTQXYXZCzmo02rHZ7xY3OS2XLAA4&s=3peP8Yp19VD8Uxq_kihX6Rmgw90SDIRCuk
> -c24oIwSY&e=
> cTAKES+4.0+-+Temporal+Module
>
> Sean
>
>
> -----Original Message-----
> From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
> Sent: Wednesday, September 13, 2017 8:21 AM
> To: Apache cTAKES Dev
> Subject: Re: ctakes timelanes [EXTERNAL]
>
> Thanks Sean. I am trying to run ctakes timelines which is present in
> ctakes demo and in sandbox.
> However do I need to use Temporal for this purpose ? I m unable to
> find any proper document on executing temporal.
>
> Regards,
> Sourabh
>
> On 08-Sep-2017 6:47 PM, "Finan, Sean"
> <Se...@childrens.harvard.edu>
> wrote:
>
> > Hi Sourabh,
> > Are you running the ctakes temporal module?
> > Sean
> > -----Original Message-----
> > From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
> > Sent: Friday, September 08, 2017 4:17 AM
> > To: Apache cTAKES Dev
> > Subject: ctakes timelanes [EXTERNAL]
> >
> > Hi,
> >
> > I followed the steps mentioned in the link "
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__mail-2Da
> > rchives.apache.org_mod-5Fmbox_ctakes-2Ddev_201603.mbox_-253C
> > F968C6DCE9D2F04CB8519CB3ACF06E99B83311B8-40ex04.net.ucsf.
> > edu-253E&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx
> > eFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > SQ9bIho3n-ylrOZIZbms-QwMLocKDSzvOPWfSbd8Plo&s=BkVeYebqURCYsp
> > T60FVz_ofTsrF9tEEmt5RQdO8WRyw&e= "
> > and without any error. I am feeding the input as the xmi file ,tried
> > with simple txt files too but couldn't see and timelines or any data
> > at all. It is just that the UI is popping up , taking the input file
> > but showing no output. Am I missing something, can somebody help me
> > to understand why there is no output. Thanks in advance for the help.
> >
> > Regards,
> > Sourabh
> >
>
Re: ctakes timelanes [EXTERNAL] [SUSPICIOUS]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
Sourabh, that is not the right way to run the temporal pipelines. That class is one we use for running evaluations on standard datasets for writing papers. You need to add the temporal components to the end of your existing pipeline (before the xmi writer part). Here is an example of how it's done using uimafit:
http://svn.apache.org/viewvc/ctakes/tags/ctakes-4.0.0/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java?view=markup
if you are using piper files or uima xml descriptors you will need to adapt these.
Tim
________________________________________
From: Finan, Sean <Se...@childrens.harvard.edu>
Sent: Friday, September 15, 2017 9:03 AM
To: dev@ctakes.apache.org
Subject: RE: ctakes timelanes [EXTERNAL] [SUSPICIOUS]
Hi Sourabh,
Does the run stop? I occasionally see that same error in another pipeline but it doesn't stop the run.
Thanks,
Sean
-----Original Message-----
From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
Sent: Friday, September 15, 2017 1:47 AM
To: Apache cTAKES Dev
Subject: Re: ctakes timelanes [EXTERNAL]
Thanks Sean. If my understanding is correct Timelanes expect an XMI input having temoral and entity information. Hence I am using ctakes temporal package to extract the info. I tried executing EvaluationOfEventTimeRelations.java with the following parameters
"--text=E:/cTakes/apache-ctakes-4.0.0/bin/testdata/input/ --format=Anafora --xml=F:/sourabhmukherjee/thymedata-master/coloncancer/Test/ID006_clinic_016/
--xmi=E:/cTakes/apache-ctakes-4.0.0/bin/testdata/ouput --kernelParams="c
0.001953125 t 0.03125 d 3 g 1.0 S 1 C + L 0.5 T 0.1 N 3" --patients=1-218 --useGoldAttributes"
But I am getting the following error when tried to run it in eclipse
Error with parameter settings:
,Kernel=tk,Cost=10.0,Gamma=1.0,secondKernel=polynomial,operator=SUM,tkWeight=0.1,lambda=0.1
org.apache.uima.resource.ResourceInitializationException: The feature org.apache.ctakes.typesystem.type.textspan.List:items is declared twice, with incompatible multipleReferencesAllowed specifications. (Descriptor:
jar:file:/E:/cTakes/apache-ctakes-4.0.0/lib/ctakes-type-system-4.0.0.jar!/org/apache/ctakes/typesystem/types/TypeSystem.xml)
at
org.apache.uima.util.CasCreationUtils.mergeFeatures(CasCreationUtils.java:1709)
at
org.apache.uima.util.CasCreationUtils.addTypeToMergedTypeSystem(CasCreationUtils.java:1178)
at
org.apache.uima.util.CasCreationUtils.mergeTypeSystems(CasCreationUtils.java:1100)
at
org.apache.uima.util.CasCreationUtils.mergeTypeSystems(CasCreationUtils.java:1029)
at
org.apache.uima.fit.factory.TypeSystemDescriptionFactory.createTypeSystemDescription(TypeSystemDescriptionFactory.java:119)
at
org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineDescription(AnalysisEngineFactory.java:978)
at
org.cleartk.util.ae.UriToDocumentTextAnnotator.getDescription(UriToDocumentTextAnnotator.java:58)
at
org.apache.ctakes.temporal.eval.Evaluation_ImplBase.getXMIReadingPreprocessorAggregateBuilder(Evaluation_ImplBase.java:471)
at
org.apache.ctakes.temporal.eval.Evaluation_ImplBase.getPreprocessorAggregateBuilder(Evaluation_ImplBase.java:464)
at
org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.train(EvaluationOfEventTimeRelations.java:303)
at
org.cleartk.eval.Evaluation_ImplBase.trainAndTest(Evaluation_ImplBase.java:76)
at
org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.main(EvaluationOfEventTimeRelations.java:211)
It would be a great help if somebody helps me here since I am new to both ctakes and Java.
Thanks in advance for your help.
Regards,
Sourabh
On Wed, Sep 13, 2017 at 9:10 AM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:
> Hi Sourabh,
>
> The timelanes gui displays temporal information extracted by ctakes on
> a timeline. That information is extracted by the ctakes-temporal module.
> Without temporal information it can still display a markup of the text
> and allow searching, etc. but is no more useful than many other
> annotation markup tools.
>
> You can find the wiki page for the temporal module here:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_
> confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS
> dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=CmDrS1CLFg
> yz2OkgTQXYXZCzmo02rHZ7xY3OS2XLAA4&s=3peP8Yp19VD8Uxq_kihX6Rmgw90SDIRCuk
> -c24oIwSY&e=
> cTAKES+4.0+-+Temporal+Module
>
> Sean
>
>
> -----Original Message-----
> From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
> Sent: Wednesday, September 13, 2017 8:21 AM
> To: Apache cTAKES Dev
> Subject: Re: ctakes timelanes [EXTERNAL]
>
> Thanks Sean. I am trying to run ctakes timelines which is present in
> ctakes demo and in sandbox.
> However do I need to use Temporal for this purpose ? I m unable to
> find any proper document on executing temporal.
>
> Regards,
> Sourabh
>
> On 08-Sep-2017 6:47 PM, "Finan, Sean"
> <Se...@childrens.harvard.edu>
> wrote:
>
> > Hi Sourabh,
> > Are you running the ctakes temporal module?
> > Sean
> > -----Original Message-----
> > From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
> > Sent: Friday, September 08, 2017 4:17 AM
> > To: Apache cTAKES Dev
> > Subject: ctakes timelanes [EXTERNAL]
> >
> > Hi,
> >
> > I followed the steps mentioned in the link "
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__mail-2Da
> > rchives.apache.org_mod-5Fmbox_ctakes-2Ddev_201603.mbox_-253C
> > F968C6DCE9D2F04CB8519CB3ACF06E99B83311B8-40ex04.net.ucsf.
> > edu-253E&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx
> > eFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > SQ9bIho3n-ylrOZIZbms-QwMLocKDSzvOPWfSbd8Plo&s=BkVeYebqURCYsp
> > T60FVz_ofTsrF9tEEmt5RQdO8WRyw&e= "
> > and without any error. I am feeding the input as the xmi file ,tried
> > with simple txt files too but couldn't see and timelines or any data
> > at all. It is just that the UI is popping up , taking the input file
> > but showing no output. Am I missing something, can somebody help me
> > to understand why there is no output. Thanks in advance for the help.
> >
> > Regards,
> > Sourabh
> >
>
RE: ctakes timelanes [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Sourabh,
Does the run stop? I occasionally see that same error in another pipeline but it doesn't stop the run.
Thanks,
Sean
-----Original Message-----
From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
Sent: Friday, September 15, 2017 1:47 AM
To: Apache cTAKES Dev
Subject: Re: ctakes timelanes [EXTERNAL]
Thanks Sean. If my understanding is correct Timelanes expect an XMI input having temoral and entity information. Hence I am using ctakes temporal package to extract the info. I tried executing EvaluationOfEventTimeRelations.java with the following parameters
"--text=E:/cTakes/apache-ctakes-4.0.0/bin/testdata/input/ --format=Anafora --xml=F:/sourabhmukherjee/thymedata-master/coloncancer/Test/ID006_clinic_016/
--xmi=E:/cTakes/apache-ctakes-4.0.0/bin/testdata/ouput --kernelParams="c
0.001953125 t 0.03125 d 3 g 1.0 S 1 C + L 0.5 T 0.1 N 3" --patients=1-218 --useGoldAttributes"
But I am getting the following error when tried to run it in eclipse
Error with parameter settings:
,Kernel=tk,Cost=10.0,Gamma=1.0,secondKernel=polynomial,operator=SUM,tkWeight=0.1,lambda=0.1
org.apache.uima.resource.ResourceInitializationException: The feature org.apache.ctakes.typesystem.type.textspan.List:items is declared twice, with incompatible multipleReferencesAllowed specifications. (Descriptor:
jar:file:/E:/cTakes/apache-ctakes-4.0.0/lib/ctakes-type-system-4.0.0.jar!/org/apache/ctakes/typesystem/types/TypeSystem.xml)
at
org.apache.uima.util.CasCreationUtils.mergeFeatures(CasCreationUtils.java:1709)
at
org.apache.uima.util.CasCreationUtils.addTypeToMergedTypeSystem(CasCreationUtils.java:1178)
at
org.apache.uima.util.CasCreationUtils.mergeTypeSystems(CasCreationUtils.java:1100)
at
org.apache.uima.util.CasCreationUtils.mergeTypeSystems(CasCreationUtils.java:1029)
at
org.apache.uima.fit.factory.TypeSystemDescriptionFactory.createTypeSystemDescription(TypeSystemDescriptionFactory.java:119)
at
org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineDescription(AnalysisEngineFactory.java:978)
at
org.cleartk.util.ae.UriToDocumentTextAnnotator.getDescription(UriToDocumentTextAnnotator.java:58)
at
org.apache.ctakes.temporal.eval.Evaluation_ImplBase.getXMIReadingPreprocessorAggregateBuilder(Evaluation_ImplBase.java:471)
at
org.apache.ctakes.temporal.eval.Evaluation_ImplBase.getPreprocessorAggregateBuilder(Evaluation_ImplBase.java:464)
at
org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.train(EvaluationOfEventTimeRelations.java:303)
at
org.cleartk.eval.Evaluation_ImplBase.trainAndTest(Evaluation_ImplBase.java:76)
at
org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.main(EvaluationOfEventTimeRelations.java:211)
It would be a great help if somebody helps me here since I am new to both ctakes and Java.
Thanks in advance for your help.
Regards,
Sourabh
On Wed, Sep 13, 2017 at 9:10 AM, Finan, Sean < Sean.Finan@childrens.harvard.edu> wrote:
> Hi Sourabh,
>
> The timelanes gui displays temporal information extracted by ctakes on
> a timeline. That information is extracted by the ctakes-temporal module.
> Without temporal information it can still display a markup of the text
> and allow searching, etc. but is no more useful than many other
> annotation markup tools.
>
> You can find the wiki page for the temporal module here:
> https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_
> confluence_display_CTAKES_&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMS
> dioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=CmDrS1CLFg
> yz2OkgTQXYXZCzmo02rHZ7xY3OS2XLAA4&s=3peP8Yp19VD8Uxq_kihX6Rmgw90SDIRCuk
> -c24oIwSY&e=
> cTAKES+4.0+-+Temporal+Module
>
> Sean
>
>
> -----Original Message-----
> From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
> Sent: Wednesday, September 13, 2017 8:21 AM
> To: Apache cTAKES Dev
> Subject: Re: ctakes timelanes [EXTERNAL]
>
> Thanks Sean. I am trying to run ctakes timelines which is present in
> ctakes demo and in sandbox.
> However do I need to use Temporal for this purpose ? I m unable to
> find any proper document on executing temporal.
>
> Regards,
> Sourabh
>
> On 08-Sep-2017 6:47 PM, "Finan, Sean"
> <Se...@childrens.harvard.edu>
> wrote:
>
> > Hi Sourabh,
> > Are you running the ctakes temporal module?
> > Sean
> > -----Original Message-----
> > From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
> > Sent: Friday, September 08, 2017 4:17 AM
> > To: Apache cTAKES Dev
> > Subject: ctakes timelanes [EXTERNAL]
> >
> > Hi,
> >
> > I followed the steps mentioned in the link "
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__mail-2Da
> > rchives.apache.org_mod-5Fmbox_ctakes-2Ddev_201603.mbox_-253C
> > F968C6DCE9D2F04CB8519CB3ACF06E99B83311B8-40ex04.net.ucsf.
> > edu-253E&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx
> > eFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > SQ9bIho3n-ylrOZIZbms-QwMLocKDSzvOPWfSbd8Plo&s=BkVeYebqURCYsp
> > T60FVz_ofTsrF9tEEmt5RQdO8WRyw&e= "
> > and without any error. I am feeding the input as the xmi file ,tried
> > with simple txt files too but couldn't see and timelines or any data
> > at all. It is just that the UI is popping up , taking the input file
> > but showing no output. Am I missing something, can somebody help me
> > to understand why there is no output. Thanks in advance for the help.
> >
> > Regards,
> > Sourabh
> >
>
Re: ctakes timelanes [EXTERNAL]
Posted by Sourabh Mukherjee <so...@gmail.com>.
Thanks Sean. If my understanding is correct Timelanes expect an XMI input
having temoral and entity information. Hence I am using ctakes temporal
package to extract the info. I tried executing
EvaluationOfEventTimeRelations.java with the following parameters
"--text=E:/cTakes/apache-ctakes-4.0.0/bin/testdata/input/ --format=Anafora
--xml=F:/sourabhmukherjee/thymedata-master/coloncancer/Test/ID006_clinic_016/
--xmi=E:/cTakes/apache-ctakes-4.0.0/bin/testdata/ouput --kernelParams="c
0.001953125 t 0.03125 d 3 g 1.0 S 1 C + L 0.5 T 0.1 N 3" --patients=1-218
--useGoldAttributes"
But I am getting the following error when tried to run it in eclipse
Error with parameter settings:
,Kernel=tk,Cost=10.0,Gamma=1.0,secondKernel=polynomial,operator=SUM,tkWeight=0.1,lambda=0.1
org.apache.uima.resource.ResourceInitializationException: The feature
org.apache.ctakes.typesystem.type.textspan.List:items is declared twice,
with incompatible multipleReferencesAllowed specifications. (Descriptor:
jar:file:/E:/cTakes/apache-ctakes-4.0.0/lib/ctakes-type-system-4.0.0.jar!/org/apache/ctakes/typesystem/types/TypeSystem.xml)
at
org.apache.uima.util.CasCreationUtils.mergeFeatures(CasCreationUtils.java:1709)
at
org.apache.uima.util.CasCreationUtils.addTypeToMergedTypeSystem(CasCreationUtils.java:1178)
at
org.apache.uima.util.CasCreationUtils.mergeTypeSystems(CasCreationUtils.java:1100)
at
org.apache.uima.util.CasCreationUtils.mergeTypeSystems(CasCreationUtils.java:1029)
at
org.apache.uima.fit.factory.TypeSystemDescriptionFactory.createTypeSystemDescription(TypeSystemDescriptionFactory.java:119)
at
org.apache.uima.fit.factory.AnalysisEngineFactory.createEngineDescription(AnalysisEngineFactory.java:978)
at
org.cleartk.util.ae.UriToDocumentTextAnnotator.getDescription(UriToDocumentTextAnnotator.java:58)
at
org.apache.ctakes.temporal.eval.Evaluation_ImplBase.getXMIReadingPreprocessorAggregateBuilder(Evaluation_ImplBase.java:471)
at
org.apache.ctakes.temporal.eval.Evaluation_ImplBase.getPreprocessorAggregateBuilder(Evaluation_ImplBase.java:464)
at
org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.train(EvaluationOfEventTimeRelations.java:303)
at
org.cleartk.eval.Evaluation_ImplBase.trainAndTest(Evaluation_ImplBase.java:76)
at
org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.main(EvaluationOfEventTimeRelations.java:211)
It would be a great help if somebody helps me here since I am new to both
ctakes and Java.
Thanks in advance for your help.
Regards,
Sourabh
On Wed, Sep 13, 2017 at 9:10 AM, Finan, Sean <
Sean.Finan@childrens.harvard.edu> wrote:
> Hi Sourabh,
>
> The timelanes gui displays temporal information extracted by ctakes on a
> timeline. That information is extracted by the ctakes-temporal module.
> Without temporal information it can still display a markup of the text and
> allow searching, etc. but is no more useful than many other annotation
> markup tools.
>
> You can find the wiki page for the temporal module here:
> https://cwiki.apache.org/confluence/display/CTAKES/
> cTAKES+4.0+-+Temporal+Module
>
> Sean
>
>
> -----Original Message-----
> From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
> Sent: Wednesday, September 13, 2017 8:21 AM
> To: Apache cTAKES Dev
> Subject: Re: ctakes timelanes [EXTERNAL]
>
> Thanks Sean. I am trying to run ctakes timelines which is present in
> ctakes demo and in sandbox.
> However do I need to use Temporal for this purpose ? I m unable to find
> any proper document on executing temporal.
>
> Regards,
> Sourabh
>
> On 08-Sep-2017 6:47 PM, "Finan, Sean" <Se...@childrens.harvard.edu>
> wrote:
>
> > Hi Sourabh,
> > Are you running the ctakes temporal module?
> > Sean
> > -----Original Message-----
> > From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
> > Sent: Friday, September 08, 2017 4:17 AM
> > To: Apache cTAKES Dev
> > Subject: ctakes timelanes [EXTERNAL]
> >
> > Hi,
> >
> > I followed the steps mentioned in the link "
> > https://urldefense.proofpoint.com/v2/url?u=http-3A__mail-2Da
> > rchives.apache.org_mod-5Fmbox_ctakes-2Ddev_201603.mbox_-253C
> > F968C6DCE9D2F04CB8519CB3ACF06E99B83311B8-40ex04.net.ucsf.
> > edu-253E&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx
> > eFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> > SQ9bIho3n-ylrOZIZbms-QwMLocKDSzvOPWfSbd8Plo&s=BkVeYebqURCYsp
> > T60FVz_ofTsrF9tEEmt5RQdO8WRyw&e= "
> > and without any error. I am feeding the input as the xmi file ,tried
> > with simple txt files too but couldn't see and timelines or any data
> > at all. It is just that the UI is popping up , taking the input file
> > but showing no output. Am I missing something, can somebody help me to
> > understand why there is no output. Thanks in advance for the help.
> >
> > Regards,
> > Sourabh
> >
>
RE: ctakes timelanes [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Sourabh,
The timelanes gui displays temporal information extracted by ctakes on a timeline. That information is extracted by the ctakes-temporal module. Without temporal information it can still display a markup of the text and allow searching, etc. but is no more useful than many other annotation markup tools.
You can find the wiki page for the temporal module here:
https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Temporal+Module
Sean
-----Original Message-----
From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
Sent: Wednesday, September 13, 2017 8:21 AM
To: Apache cTAKES Dev
Subject: Re: ctakes timelanes [EXTERNAL]
Thanks Sean. I am trying to run ctakes timelines which is present in ctakes demo and in sandbox.
However do I need to use Temporal for this purpose ? I m unable to find any proper document on executing temporal.
Regards,
Sourabh
On 08-Sep-2017 6:47 PM, "Finan, Sean" <Se...@childrens.harvard.edu>
wrote:
> Hi Sourabh,
> Are you running the ctakes temporal module?
> Sean
> -----Original Message-----
> From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
> Sent: Friday, September 08, 2017 4:17 AM
> To: Apache cTAKES Dev
> Subject: ctakes timelanes [EXTERNAL]
>
> Hi,
>
> I followed the steps mentioned in the link "
> https://urldefense.proofpoint.com/v2/url?u=http-3A__mail-2Da
> rchives.apache.org_mod-5Fmbox_ctakes-2Ddev_201603.mbox_-253C
> F968C6DCE9D2F04CB8519CB3ACF06E99B83311B8-40ex04.net.ucsf.
> edu-253E&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx
> eFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> SQ9bIho3n-ylrOZIZbms-QwMLocKDSzvOPWfSbd8Plo&s=BkVeYebqURCYsp
> T60FVz_ofTsrF9tEEmt5RQdO8WRyw&e= "
> and without any error. I am feeding the input as the xmi file ,tried
> with simple txt files too but couldn't see and timelines or any data
> at all. It is just that the UI is popping up , taking the input file
> but showing no output. Am I missing something, can somebody help me to
> understand why there is no output. Thanks in advance for the help.
>
> Regards,
> Sourabh
>
Re: ctakes timelanes [EXTERNAL]
Posted by Sourabh Mukherjee <so...@gmail.com>.
Thanks Sean. I am trying to run ctakes timelines which is present in ctakes
demo and in sandbox.
However do I need to use Temporal for this purpose ? I m unable to find any
proper document on executing temporal.
Regards,
Sourabh
On 08-Sep-2017 6:47 PM, "Finan, Sean" <Se...@childrens.harvard.edu>
wrote:
> Hi Sourabh,
> Are you running the ctakes temporal module?
> Sean
> -----Original Message-----
> From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
> Sent: Friday, September 08, 2017 4:17 AM
> To: Apache cTAKES Dev
> Subject: ctakes timelanes [EXTERNAL]
>
> Hi,
>
> I followed the steps mentioned in the link "
> https://urldefense.proofpoint.com/v2/url?u=http-3A__mail-2Da
> rchives.apache.org_mod-5Fmbox_ctakes-2Ddev_201603.mbox_-253C
> F968C6DCE9D2F04CB8519CB3ACF06E99B83311B8-40ex04.net.ucsf.
> edu-253E&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppx
> eFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=
> SQ9bIho3n-ylrOZIZbms-QwMLocKDSzvOPWfSbd8Plo&s=BkVeYebqURCYsp
> T60FVz_ofTsrF9tEEmt5RQdO8WRyw&e= "
> and without any error. I am feeding the input as the xmi file ,tried with
> simple txt files too but couldn't see and timelines or any data at all. It
> is just that the UI is popping up , taking the input file but showing no
> output. Am I missing something, can somebody help me to understand why
> there is no output. Thanks in advance for the help.
>
> Regards,
> Sourabh
>
RE: ctakes timelanes [EXTERNAL]
Posted by "Finan, Sean" <Se...@childrens.harvard.edu>.
Hi Sourabh,
Are you running the ctakes temporal module?
Sean
-----Original Message-----
From: Sourabh Mukherjee [mailto:sourabhbms@gmail.com]
Sent: Friday, September 08, 2017 4:17 AM
To: Apache cTAKES Dev
Subject: ctakes timelanes [EXTERNAL]
Hi,
I followed the steps mentioned in the link "
https://urldefense.proofpoint.com/v2/url?u=http-3A__mail-2Darchives.apache.org_mod-5Fmbox_ctakes-2Ddev_201603.mbox_-253CF968C6DCE9D2F04CB8519CB3ACF06E99B83311B8-40ex04.net.ucsf.edu-253E&d=DwIBaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=SQ9bIho3n-ylrOZIZbms-QwMLocKDSzvOPWfSbd8Plo&s=BkVeYebqURCYspT60FVz_ofTsrF9tEEmt5RQdO8WRyw&e= "
and without any error. I am feeding the input as the xmi file ,tried with simple txt files too but couldn't see and timelines or any data at all. It is just that the UI is popping up , taking the input file but showing no output. Am I missing something, can somebody help me to understand why there is no output. Thanks in advance for the help.
Regards,
Sourabh