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From Anirban Chakraborti <chakraborti.anir...@googlemail.com>
Subject Re: cTAKES Information Extraction
Date Tue, 20 May 2014 12:37:12 GMT
Vijay,

Pardon my ignorance.

Is Ytex an add on module for Ctakes. How do I add it.
whats the additional functionality provided by Ytex.


On Tue, May 20, 2014 at 6:02 PM, vijay garla <vngarla@gmail.com> wrote:

> YTEX writes uima annotations and the CAS to a database (MySQL/SQL
> Server/Oracle); see:
> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.1.2+YTEX+DBConsumer
>
>
>
> On Mon, May 19, 2014 at 4:25 PM, Masanz, James J. <Masanz.James@mayo.edu>wrote:
>
>>  You could try looking at
>>
>>
>>
>> org.spin.scrubber.uima.consumer.JDBCCasConsumer
>>
>>
>>
>> That’s in sandbox, not in trunk:
>>
>>
>> https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-scrubber-deid/src/main/java/org/spin/scrubber/uima/consumer/JDBCCasConsumer.java
>>
>>
>>
>>
>>
>> There’s also something in the ctakes-gui project, which is also under
>> sandbox. Pei would be the best person to give you pointers to basing off
>> that.
>>
>>
>>
>> -- James
>>
>>
>>
>> *From:* Anirban Chakraborti [mailto:chakraborti.anirban@googlemail.com]
>> *Sent:* Saturday, May 17, 2014 11:48 AM
>> *To:* user@ctakes.apache.org
>> *Subject:* RE: cTAKES Information Extraction
>>
>>
>>
>> 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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