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From Anirban Chakraborti <chakraborti.anir...@googlemail.com>
Subject RE: cTAKES Information Extraction
Date Sat, 17 May 2014 16:47:40 GMT
James,
Is there any code snippet for writing to a database from annotated cas

Pls point the same out. The one snippet I got had known type info but what
if the type is not known in advance.

Anirban
On 17 May 2014 22:08, "Masanz, James J." <Masanz.James@mayo.edu> wrote:

>  This was fixed in trunk under
>
> https://issues.apache.org/jira/browse/CTAKES-288
>
> and will be available in the next release
>
>
>
> (I was able to view the image, thanks for including your link)
>
>
>
> Code that changed is here:
>
>
>
>
> https://svn.apache.org/viewvc/ctakes/trunk/ctakes-template-filler/src/main/java/org/apache/ctakes/template/filler/ae/TemplateFillerAnnotator.java?view=markup&pathrev=1579707
>
>
>
> *From:* Tamzidur Rahman [mailto:u5184041@anu.edu.au]
> *Sent:* Thursday, May 15, 2014 6:36 AM
> *To:* user@ctakes.apache.org
> *Subject:* RE: cTAKES Information Extraction
>
>
>
> 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 <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>
> *Sent:* Monday, 12 May 2014 12:00 AM
> *To:* 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>
> 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>
> *Sent:* Sunday, 11 May 2014 11:02 PM
>
>
> *To:* 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>
> 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>
> *Sent:* Sunday, 11 May 2014 10:51 PM
> *To:* 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>
> 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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