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 >> >> >> >> >> >> >> >> >> > >
