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: Tamzidur Rahman Sent: Thursday, 15 May 2014 9:36 PM To: [email protected] 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. <[email protected]> Sent: Wednesday, 14 May 2014 5:47 AM To: '[email protected]' 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:[email protected]] Sent: Sunday, May 11, 2014 9:16 AM To: [email protected] 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 <[email protected]<mailto:[email protected]>> Sent: Monday, 12 May 2014 12:00 AM To: [email protected]<mailto:[email protected]> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> Sent: Sunday, 11 May 2014 11:02 PM To: [email protected]<mailto:[email protected]> 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 <[email protected]<mailto:[email protected]>> 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 <[email protected]<mailto:[email protected]>> Sent: Sunday, 11 May 2014 10:51 PM To: [email protected]<mailto:[email protected]> 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 <[email protected]<mailto:[email protected]>> 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
