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:[email protected]] Sent: Tuesday, March 20, 2018 2:48 PM To: [email protected] 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'; [email protected] > 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:[email protected]] > Sent: Monday, August 14, 2017 4:51 PM > To: [email protected] > 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 <[email protected]> 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 | ✉ [email protected] > > >
