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Posted to user@ctakes.apache.org by "Savova, Guergana" <Gu...@childrens.harvard.edu> on 2017/08/14 20:56:10 UTC
RE: Extract relation among entities in cTAKES [EXTERNAL]
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 [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