Re: Extract relation among entities in cTAKES [EXTERNAL]

["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 [EXTERNAL]

["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
> 
> 
>