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From Tamzidur Rahman <u5184...@anu.edu.au>
Subject RE: cTAKES Information Extraction
Date Thu, 15 May 2014 11:36:27 GMT
Sorry about the late response. The sentence that I am using is:


 "patient took 50mg of aspirin for severe pain in right knee."


I have also used the template filler as well for this sentence and I can see it identify the
locationOf and degreeOf in the CVD. However, I don't see it assign the values inside the identified
annotation for locationOf and degreeOf like the ctakes keynote suggests it should.


Here are my results for template filler using the sentence above:


http://i.imgur.com/dvq958l.png


I'm not exactly sure if you guys can see these links, so if you guys can't let me know.


Also If I had to manually extract and place these relations into the identified annotations
is there someplace I can be led to? As it is, I don't know where to start looking for the
functions that extract these values (degreeOF and locationOf).



________________________________
From: Masanz, James J. <Masanz.James@mayo.edu>
Sent: Wednesday, 14 May 2014 5:47 AM
To: 'user@ctakes.apache.org'
Subject: RE: cTAKES Information Extraction

Do you have an example that you can share of the sentences you were expecting to find locationOf
and degreeOf.

Note:
The relation extractor creates a relation between two IdentifiedAnnotation, but does not assign
values to the locationOf or degreeOf in any IdentifiedAnnotation.
The template filler assigns values to the locationOf or degreeOf based on what the relation
extractor finds.

The AggregateTemplateFiller AE contains the relation extractor and the template filler.


From: Tamzidur Rahman [mailto:u5184041@anu.edu.au]
Sent: Sunday, May 11, 2014 9:16 AM
To: user@ctakes.apache.org
Subject: RE: cTAKES Information Extraction


Thanks for the clarification Timothy. We could live without some features, however somethings
such as date, dose, even locationOf are required for our project.



As of right now locationOf or degreeOf are not related to Identified Annotations by the relation
extractor, which was what I expected as results from this key note.



https://uima.apache.org/downloads/gscl2013/keynote_ctakes.pdf page 68



a smaller link:



http://i.imgur.com/Gs3lYyS.png





________________________________
From: Anirban Chakraborti <chakraborti.anirban@googlemail.com<mailto:chakraborti.anirban@googlemail.com>>
Sent: Monday, 12 May 2014 12:00 AM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
Subject: Re: cTAKES Information Extraction

that's the desired output. What were you anticipating.

On Sun, May 11, 2014 at 6:57 PM, Tamzidur Rahman <u5184041@anu.edu.au<mailto:u5184041@anu.edu.au>>
wrote:

I have used ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextProcessor.xml
for this.



Without UMLS:

http://i.imgur.com/TWg1kzG.png



With UMLS:

http://i.imgur.com/btZdNtS.png



I am still having the same issue.



________________________________
From: Anirban Chakraborti <chakraborti.anirban@googlemail.com<mailto:chakraborti.anirban@googlemail.com>>
Sent: Sunday, 11 May 2014 11:02 PM

To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
Subject: Re: cTAKES Information Extraction

Startwith AggregatePlainText.xml , you should get annotations on target text

On Sun, May 11, 2014 at 6:30 PM, Tamzidur Rahman <u5184041@anu.edu.au<mailto:u5184041@anu.edu.au>>
wrote:

Thanks for the reply,



I haven't created any custom AEs, I've only used the default AE found in the vanilla install.



The AEs I've used:



ctakes-clinical-pipeline/desc/analysis_engine/AggregatePlaintextUMLSProcessor.xml

ctakes-relation-extractor/desc/analysis_engine/RelationExtractorAggregate



ctakes-template-filler/desc/analysis_engine/AggregateTemplateFiller





________________________________
From: Anirban Chakraborti <chakraborti.anirban@googlemail.com<mailto:chakraborti.anirban@googlemail.com>>
Sent: Sunday, 11 May 2014 10:51 PM
To: user@ctakes.apache.org<mailto:user@ctakes.apache.org>
Subject: Re: cTAKES Information Extraction

Tam,

What AE engines are you using. There might be an issue there.

On Sun, May 11, 2014 at 2:38 PM, Tamzidur Rahman <u5184041@anu.edu.au<mailto:u5184041@anu.edu.au>>
wrote:
Hi,

I've been working on a project which uses cTAKES annotations for a search algorithm in a database.
What we would like to extract is information such as body Laterality, alleviating Factor,
etc.
We've been using cTAKES CVD with various AE but we seem to be mostly producing annotations
with no information. I have used an working sample from a keynote on cTAKES as evidence of
this problem.
Working sample
    https://uima.apache.org/downloads/gscl2013/keynote_ctakes.pdf page 68

Running with sample input
    http://i.imgur.com/3n6WyHE.png

Any help would be appreciated.

Thanks






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