YTEX has recently been added to ctakes (trunk); it will be included in the coming ctakes 3.1.2 release. For more information, refer to https://cwiki.apache.org/confluence/display/CTAKES/YTEX+3.2
On Tue, May 20, 2014 at 8:37 AM, Anirban Chakraborti < [email protected]> wrote: > 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 <[email protected]> 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. >> <[email protected]>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:[email protected]] >>> *Sent:* Saturday, May 17, 2014 11:48 AM >>> *To:* [email protected] >>> *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." <[email protected]> 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:[email protected]] >>> *Sent:* Thursday, May 15, 2014 6:36 AM >>> *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]<[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]> >>> *Sent:* Monday, 12 May 2014 12:00 AM >>> *To:* [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]> >>> 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]> >>> *Sent:* Sunday, 11 May 2014 11:02 PM >>> >>> >>> *To:* [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]> >>> 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]> >>> *Sent:* Sunday, 11 May 2014 10:51 PM >>> *To:* [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]> >>> 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 >>> >>> >>> >>> >>> >>> >>> >>> >>> >> >> >
