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 > > > > > > > > >
