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Posted to user@ctakes.apache.org by Liam Bui <lb...@phemi.com> on 2017/08/14 18:28:59 UTC
Extract relation among entities in cTAKES
Hi,
I want to extract relation among entities using cTAKES, eg. procedure is
carried on which anatomicalSite, SignSymptom occurs on which anatomicalSite
and is part of which DiseaseDisorder.
Based on cTAKES sourcecode, it seems these classes (DiseaseDisroder,
Procedure, etc do support such relation through several attributes
bodySite, associatedSignSymptom, etc). However, I do not know which cTAKES
component or analysis engine that I should use to get these info.
I also notice there is cTAKES Relation Extraction component, but I have no
idea how to get it running.
Does anyone happen to have insight on these topics? Thank you!
--
Regards,
Liam Bui
☎ (604) 352-1568 | ✉ lbui@phemi.com
Re: Extract relation among entities in cTAKES
Posted by "Schenk, Gundolf" <Gu...@ucsf.edu>.
I would be very interested to learn more about his, too. Any insight appreciated. Thanks!
From: "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>
Reply-To: "user@ctakes.apache.org" <us...@ctakes.apache.org>
Date: Tuesday, March 20, 2018 at 11:11
To: "'user@ctakes.apache.org'" <us...@ctakes.apache.org>
Subject: RE: Extract relation among entities in cTAKES
It seems Liam’s email account is dead. Can anyone else can shed light on this?
From: Mullane, Sean *HS
Sent: Tuesday, March 20, 2018 2:03 PM
To: 'Liam Bui'; user@ctakes.apache.org
Subject: RE: Extract relation among entities in cTAKES
Liam,
Can you share your descriptor file? I am also trying to get the bodyLocation attribute for Identified Annotations but have so far not been successful in getting it to show up attached to the Identified Annotation.
Any other help/suggestions would be great as well.
Thanks,
Sean
From: Liam Bui [mailto:lbui@phemi.com]
Sent: Monday, August 14, 2017 4:51 PM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: Extract relation among entities in cTAKES
After experimenting with cTAKES RelationExtraction, I managed to get it working. It turns out I need to specify the model file:
builder.add( AnalysisEngineFactory.createEngineDescription(LocationOfRelationExtractorAnnotator.class,
"classifierJarPath", "/org/apache/ctakes/relationextractor/models/location_of/model.jar") );
With that, I manged to extract "bodyLocation" for each Identified Annotation.
How about "associatedSignSymptom"? I couldn't find any AnalysisEngine that would outputs this attribute.
Thanks.
On Mon, Aug 14, 2017 at 11:28 AM, Liam Bui <lb...@phemi.com>> wrote:
Hi,
I want to extract relation among entities using cTAKES, eg. procedure is carried on which anatomicalSite, SignSymptom occurs on which anatomicalSite and is part of which DiseaseDisorder.
Based on cTAKES sourcecode, it seems these classes (DiseaseDisroder, Procedure, etc do support such relation through several attributes bodySite, associatedSignSymptom, etc). However, I do not know which cTAKES component or analysis engine that I should use to get these info.
I also notice there is cTAKES Relation Extraction component, but I have no idea how to get it running.
Does anyone happen to have insight on these topics? Thank you!
--
Regards,
Liam Bui
☎ (604) 352-1568<tel:(604)%20352-1568> | ✉ lbui@phemi.com<ma...@phemi.com>
RE: Extract relation among entities in cTAKES [EXTERNAL]
Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.
At this point I have gotten as far as creating LocationOfTextRelations and the RelationArguments that they reference, and also having the LocationOfTextRelations annotations filled in as the bodyLocation attribute in the IdentifiedAnnotations. I had to add the TemplateFillerAnnotator (whose .jar was missing from the user distribution of 4.0.0, incidentally) at the end of the pipeline to get the bodyLocation filled in.
However I haven't yet succeeded in getting the relations to write to the database (I'm using the DBConsumer from YTEX for database output). I have created tables for them per the https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2.0+-+YTEX+DBConsumer page in the wiki but so far they're empty. Other annotation types can be added so I know it can be done (e.g. I have added AnatomicalSite by following that wiki page).
I can see the relation outputs if I use the XMI writer consumer, so I know they're being created.
Sean
-----Original Message-----
From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
Sent: Tuesday, March 20, 2018 2:48 PM
To: user@ctakes.apache.org
Subject: Re: Extract relation among entities in cTAKES [EXTERNAL]
I just want to clarify one thing -- you say you can't get it to show up attached to the IdentifiedAnnotation. Just to be clear, there should be a separate annotation type called LocationOfTextRelation, with two arguments. I don't know if a bodyLocation attribute is ever populated.
Can you check whether you see that relation type?
Tim
On Tue, 2018-03-20 at 18:08 +0000, Mullane, Sean *HS wrote:
> It seems Liam’s email account is dead. Can anyone else can shed light
> on this?
>
> From: Mullane, Sean *HS
> Sent: Tuesday, March 20, 2018 2:03 PM
> To: 'Liam Bui'; user@ctakes.apache.org
> Subject: RE: Extract relation among entities in cTAKES
>
> Liam,
>
> Can you share your descriptor file? I am also trying to get the
> bodyLocation attribute for Identified Annotations but have so far not
> been successful in getting it to show up attached to the Identified
> Annotation.
>
> Any other help/suggestions would be great as well.
>
> Thanks,
> Sean
>
> From: Liam Bui [mailto:lbui@phemi.com]
> Sent: Monday, August 14, 2017 4:51 PM
> To: user@ctakes.apache.org
> Subject: Re: Extract relation among entities in cTAKES
>
> After experimenting with cTAKES RelationExtraction, I managed to get
> it working. It turns out I need to specify the model file:
> builder.add(
> AnalysisEngineFactory.createEngineDescription(LocationOfRelationExtra
> ctorAnnotator.class,
> "classifierJarPath",
> "/org/apache/ctakes/relationextractor/models/location_of/model.jar")
> );
>
> With that, I manged to extract "bodyLocation" for each Identified
> Annotation.
> How about "associatedSignSymptom"? I couldn't find any AnalysisEngine
> that would outputs this attribute.
>
> Thanks.
>
> On Mon, Aug 14, 2017 at 11:28 AM, Liam Bui <lb...@phemi.com> wrote:
> Hi,
>
> I want to extract relation among entities using cTAKES, eg. procedure
> is carried on which anatomicalSite, SignSymptom occurs on which
> anatomicalSite and is part of which DiseaseDisorder.
>
> Based on cTAKES sourcecode, it seems these classes (DiseaseDisroder,
> Procedure, etc do support such relation through several attributes
> bodySite, associatedSignSymptom, etc). However, I do not know which
> cTAKES component or analysis engine that I should use to get these
> info.
>
> I also notice there is cTAKES Relation Extraction component, but I
> have no idea how to get it running.
>
> Does anyone happen to have insight on these topics? Thank you!
>
> --
> Regards,
> Liam Bui
> ☎ (604) 352-1568 | ✉ lbui@phemi.com
>
>
>
Re: Extract relation among entities in cTAKES [EXTERNAL]
Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.
I just want to clarify one thing -- you say you can't get it to show up
attached to the IdentifiedAnnotation. Just to be clear, there should be
a separate annotation type called LocationOfTextRelation, with two
arguments. I don't know if a bodyLocation attribute is ever populated.
Can you check whether you see that relation type?
Tim
On Tue, 2018-03-20 at 18:08 +0000, Mullane, Sean *HS wrote:
> It seems Liam’s email account is dead. Can anyone else can shed light
> on this?
>
> From: Mullane, Sean *HS
> Sent: Tuesday, March 20, 2018 2:03 PM
> To: 'Liam Bui'; user@ctakes.apache.org
> Subject: RE: Extract relation among entities in cTAKES
>
> Liam,
>
> Can you share your descriptor file? I am also trying to get the
> bodyLocation attribute for Identified Annotations but have so far not
> been successful in getting it to show up attached to the Identified
> Annotation.
>
> Any other help/suggestions would be great as well.
>
> Thanks,
> Sean
>
> From: Liam Bui [mailto:lbui@phemi.com]
> Sent: Monday, August 14, 2017 4:51 PM
> To: user@ctakes.apache.org
> Subject: Re: Extract relation among entities in cTAKES
>
> After experimenting with cTAKES RelationExtraction, I managed to get
> it working. It turns out I need to specify the model file:
> builder.add(
> AnalysisEngineFactory.createEngineDescription(LocationOfRelationExtra
> ctorAnnotator.class,
> "classifierJarPath",
> "/org/apache/ctakes/relationextractor/models/location_of/model.jar")
> );
>
> With that, I manged to extract "bodyLocation" for each Identified
> Annotation.
> How about "associatedSignSymptom"? I couldn't find any AnalysisEngine
> that would outputs this attribute.
>
> Thanks.
>
> On Mon, Aug 14, 2017 at 11:28 AM, Liam Bui <lb...@phemi.com> wrote:
> Hi,
>
> I want to extract relation among entities using cTAKES, eg. procedure
> is carried on which anatomicalSite, SignSymptom occurs on which
> anatomicalSite and is part of which DiseaseDisorder.
>
> Based on cTAKES sourcecode, it seems these classes (DiseaseDisroder,
> Procedure, etc do support such relation through several attributes
> bodySite, associatedSignSymptom, etc). However, I do not know which
> cTAKES component or analysis engine that I should use to get these
> info.
>
> I also notice there is cTAKES Relation Extraction component, but I
> have no idea how to get it running.
>
> Does anyone happen to have insight on these topics? Thank you!
>
> --
> Regards,
> Liam Bui
> ☎ (604) 352-1568 | ✉ lbui@phemi.com
>
>
>
RE: Extract relation among entities in cTAKES
Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.
It seems Liam’s email account is dead. Can anyone else can shed light on this?
From: Mullane, Sean *HS
Sent: Tuesday, March 20, 2018 2:03 PM
To: 'Liam Bui'; user@ctakes.apache.org
Subject: RE: Extract relation among entities in cTAKES
Liam,
Can you share your descriptor file? I am also trying to get the bodyLocation attribute for Identified Annotations but have so far not been successful in getting it to show up attached to the Identified Annotation.
Any other help/suggestions would be great as well.
Thanks,
Sean
From: Liam Bui [mailto:lbui@phemi.com]
Sent: Monday, August 14, 2017 4:51 PM
To: user@ctakes.apache.org<ma...@ctakes.apache.org>
Subject: Re: Extract relation among entities in cTAKES
After experimenting with cTAKES RelationExtraction, I managed to get it working. It turns out I need to specify the model file:
builder.add( AnalysisEngineFactory.createEngineDescription(LocationOfRelationExtractorAnnotator.class,
"classifierJarPath", "/org/apache/ctakes/relationextractor/models/location_of/model.jar") );
With that, I manged to extract "bodyLocation" for each Identified Annotation.
How about "associatedSignSymptom"? I couldn't find any AnalysisEngine that would outputs this attribute.
Thanks.
On Mon, Aug 14, 2017 at 11:28 AM, Liam Bui <lb...@phemi.com>> wrote:
Hi,
I want to extract relation among entities using cTAKES, eg. procedure is carried on which anatomicalSite, SignSymptom occurs on which anatomicalSite and is part of which DiseaseDisorder.
Based on cTAKES sourcecode, it seems these classes (DiseaseDisroder, Procedure, etc do support such relation through several attributes bodySite, associatedSignSymptom, etc). However, I do not know which cTAKES component or analysis engine that I should use to get these info.
I also notice there is cTAKES Relation Extraction component, but I have no idea how to get it running.
Does anyone happen to have insight on these topics? Thank you!
--
Regards,
Liam Bui
☎ (604) 352-1568<tel:(604)%20352-1568> | ✉ lbui@phemi.com<ma...@phemi.com>
RE: Extract relation among entities in cTAKES
Posted by "Mullane, Sean *HS" <SP...@hscmail.mcc.virginia.edu>.
Liam,
Can you share your descriptor file? I am also trying to get the bodyLocation attribute for Identified Annotations but have so far not been successful in getting it to show up attached to the Identified Annotation.
Any other help/suggestions would be great as well.
Thanks,
Sean
From: Liam Bui [mailto:lbui@phemi.com]
Sent: Monday, August 14, 2017 4:51 PM
To: user@ctakes.apache.org
Subject: Re: Extract relation among entities in cTAKES
After experimenting with cTAKES RelationExtraction, I managed to get it working. It turns out I need to specify the model file:
builder.add( AnalysisEngineFactory.createEngineDescription(LocationOfRelationExtractorAnnotator.class,
"classifierJarPath", "/org/apache/ctakes/relationextractor/models/location_of/model.jar") );
With that, I manged to extract "bodyLocation" for each Identified Annotation.
How about "associatedSignSymptom"? I couldn't find any AnalysisEngine that would outputs this attribute.
Thanks.
On Mon, Aug 14, 2017 at 11:28 AM, Liam Bui <lb...@phemi.com>> wrote:
Hi,
I want to extract relation among entities using cTAKES, eg. procedure is carried on which anatomicalSite, SignSymptom occurs on which anatomicalSite and is part of which DiseaseDisorder.
Based on cTAKES sourcecode, it seems these classes (DiseaseDisroder, Procedure, etc do support such relation through several attributes bodySite, associatedSignSymptom, etc). However, I do not know which cTAKES component or analysis engine that I should use to get these info.
I also notice there is cTAKES Relation Extraction component, but I have no idea how to get it running.
Does anyone happen to have insight on these topics? Thank you!
--
Regards,
Liam Bui
☎ (604) 352-1568<tel:(604)%20352-1568> | ✉ lbui@phemi.com<ma...@phemi.com>
Re: Extract relation among entities in cTAKES [EXTERNAL]
Posted by Liam Bui <lb...@phemi.com>.
Hi Guergana,
Thanks a lot for the clarification! The article is really helpful.
On Mon, Aug 14, 2017 at 1:56 PM, Savova, Guergana <
Guergana.Savova@childrens.harvard.edu> wrote:
> Hi Liam,
>
>
>
> associatedSignSymptom has not been implemented yet.
>
>
>
> More details of the relation extraction module are in
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994852/
>
> I hope this helps you.
>
>
>
> Kindest regards,
>
> --Guergana
>
>
>
> Guergana Savova, PhD, FACMI
> Associate Professor
> PI Natural Language Processing Lab
> Boston Children's Hospital and Harvard Medical School
> 300 Longwood Avenue
> Mailstop: BCH3092
> Enders 144.1
> Boston, MA 02115
> Tel: (617) 919-2972
> Fax: (617) 730-0817
> Guergana.Savova@childrens.harvard.edu
> Harvard Scholar: http://scholar.harvard.edu/guergana_k_savova/biocv
>
> http://ctakes.apache.org
>
> http://thyme.healthnlp.org
>
> http://cancer.healthnlp.org
>
> http://share.healthnlp.org
>
> http://center.healthnlp.org
>
>
>
>
>
> *From:* Liam Bui [mailto:lbui@phemi.com]
> *Sent:* Monday, August 14, 2017 4:51 PM
> *To:* user@ctakes.apache.org
> *Subject:* Re: Extract relation among entities in cTAKES [EXTERNAL]
>
>
>
> After experimenting with cTAKES RelationExtraction, I managed to get it
> working. It turns out I need to specify the model file:
>
> builder.add( AnalysisEngineFactory.*createEngineDescription*(LocationOfRelationExtractorAnnotator.*class*,
> *"classifierJarPath"*, *"/org/apache/ctakes/relationextractor/models/location_of/model.jar"*) );
>
>
>
> With that, I manged to extract "bodyLocation" for each Identified
> Annotation.
>
> How about "associatedSignSymptom"? I couldn't find any AnalysisEngine that
> would outputs this attribute.
>
>
>
> Thanks.
>
>
>
> On Mon, Aug 14, 2017 at 11:28 AM, Liam Bui <lb...@phemi.com> wrote:
>
> Hi,
>
>
>
> I want to extract relation among entities using cTAKES, eg. procedure is
> carried on which anatomicalSite, SignSymptom occurs on which anatomicalSite
> and is part of which DiseaseDisorder.
>
>
>
> Based on cTAKES sourcecode, it seems these classes (DiseaseDisroder,
> Procedure, etc do support such relation through several attributes
> bodySite, associatedSignSymptom, etc). However, I do not know which cTAKES
> component or analysis engine that I should use to get these info.
>
>
>
> I also notice there is cTAKES Relation Extraction component, but I have no
> idea how to get it running.
>
>
>
> Does anyone happen to have insight on these topics? Thank you!
>
>
>
> --
>
> Regards,
>
> Liam Bui
>
> ☎ (604) 352-1568 | ✉ lbui@phemi.com
>
>
>
>
>
--
Regards,
Liam Bui
☎ (604) 352-1568 | ✉ lbui@phemi.com
RE: Extract relation among entities in cTAKES [EXTERNAL]
Posted by "Savova, Guergana" <Gu...@childrens.harvard.edu>.
Hi Liam,
associatedSignSymptom has not been implemented yet.
More details of the relation extraction module are in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994852/
I hope this helps you.
Kindest regards,
--Guergana
Guergana Savova, PhD, FACMI
Associate Professor
PI Natural Language Processing Lab
Boston Children's Hospital and Harvard Medical School
300 Longwood Avenue
Mailstop: BCH3092
Enders 144.1
Boston, MA 02115
Tel: (617) 919-2972
Fax: (617) 730-0817
Guergana.Savova@childrens.harvard.edu<ma...@childrens.harvard.edu>
Harvard Scholar: http://scholar.harvard.edu/guergana_k_savova/biocv
http://ctakes.apache.org<http://ctakes.apache.org/>
http://thyme.healthnlp.org<http://thyme.healthnlp.org/>
http://cancer.healthnlp.org<http://cancer.healthnlp.org/>
http://share.healthnlp.org<http://share.healthnlp.org/>
http://center.healthnlp.org<http://center.healthnlp.org/>
From: Liam Bui [mailto:lbui@phemi.com]
Sent: Monday, August 14, 2017 4:51 PM
To: user@ctakes.apache.org
Subject: Re: Extract relation among entities in cTAKES [EXTERNAL]
After experimenting with cTAKES RelationExtraction, I managed to get it working. It turns out I need to specify the model file:
builder.add( AnalysisEngineFactory.createEngineDescription(LocationOfRelationExtractorAnnotator.class,
"classifierJarPath", "/org/apache/ctakes/relationextractor/models/location_of/model.jar") );
With that, I manged to extract "bodyLocation" for each Identified Annotation.
How about "associatedSignSymptom"? I couldn't find any AnalysisEngine that would outputs this attribute.
Thanks.
On Mon, Aug 14, 2017 at 11:28 AM, Liam Bui <lb...@phemi.com>> wrote:
Hi,
I want to extract relation among entities using cTAKES, eg. procedure is carried on which anatomicalSite, SignSymptom occurs on which anatomicalSite and is part of which DiseaseDisorder.
Based on cTAKES sourcecode, it seems these classes (DiseaseDisroder, Procedure, etc do support such relation through several attributes bodySite, associatedSignSymptom, etc). However, I do not know which cTAKES component or analysis engine that I should use to get these info.
I also notice there is cTAKES Relation Extraction component, but I have no idea how to get it running.
Does anyone happen to have insight on these topics? Thank you!
--
Regards,
Liam Bui
☎ (604) 352-1568<tel:(604)%20352-1568> | ✉ lbui@phemi.com<ma...@phemi.com>
Re: Extract relation among entities in cTAKES
Posted by Liam Bui <lb...@phemi.com>.
After experimenting with cTAKES RelationExtraction, I managed to get it
working. It turns out I need to specify the model file:
builder.add( AnalysisEngineFactory.createEngineDescription(LocationOfRelationExtractorAnnotator.class,
"classifierJarPath",
"/org/apache/ctakes/relationextractor/models/location_of/model.jar")
);
With that, I manged to extract "bodyLocation" for each Identified
Annotation.
How about "associatedSignSymptom"? I couldn't find any AnalysisEngine that
would outputs this attribute.
Thanks.
On Mon, Aug 14, 2017 at 11:28 AM, Liam Bui <lb...@phemi.com> wrote:
> Hi,
>
> I want to extract relation among entities using cTAKES, eg. procedure is
> carried on which anatomicalSite, SignSymptom occurs on which anatomicalSite
> and is part of which DiseaseDisorder.
>
> Based on cTAKES sourcecode, it seems these classes (DiseaseDisroder,
> Procedure, etc do support such relation through several attributes
> bodySite, associatedSignSymptom, etc). However, I do not know which cTAKES
> component or analysis engine that I should use to get these info.
>
> I also notice there is cTAKES Relation Extraction component, but I have no
> idea how to get it running.
>
> Does anyone happen to have insight on these topics? Thank you!
>
> --
> Regards,
> Liam Bui
> ☎ (604) 352-1568 | ✉ lbui@phemi.com
>