Glad you didn't encounter any issues. As far as getting it running there wasn't any particular issue, my worry is just the 'unknown unknowns' as they say. I think for performance I have one worry yet, especially if it is the default sectionizer -- does it fail gracefully and will it ever skip text? I think it should be ok but that would be one thing it would be worth testing. So, Paula, what happens if you change the spelling of a section header (i.e., introduce a typo)? And just out of curiosity, what kind of notes are you running it on? Any particular dataset? Thanks Tim
On 12/05/2013 09:04 PM, digital paula wrote: Pei, I appreciate you mentioning the preferredText feature for getting section headings to render, the first column in the mapping file should suffice. In a previous post, Tim stated that the sectionizer would be a huge benefit to the research community once it's working or something along those lines. What was the problem with getting it to work? I ask because I didn't encounter any issues during my preliminary testing. All I did was an integration and minor configuration, as stated in my previous post. The reason why I'd like to know is so I'm cognizant of any known issues in case I encounter them once I get back to using the sectionizer...should be in a few days. Thanks. Regards, Paula ________________________________ From: [email protected]<mailto:[email protected]> To: [email protected]<mailto:[email protected]> Subject: RE: cTAKES Sectionizer: how to integrate it with clinical pipeline - Solved Date: Thu, 5 Dec 2013 14:26:56 +0000 Paula, Glad to hear it’s working for you. Please feel free to let us know how it works out for you in your use case and dataset. >I didn't see it in the trunk so I manually added the text file >ccda_sections.txt taken from the sandbox. I added it under >src/main/resources in ctakes-core: org/apache/ctakes/core/sections/ccda_sections.txt Check out: http://svn.apache.org/r1547576 ctakes/trunk/ctakes-core-res/src/main/resources/org/apache/ctakes/core/sections/ccda_sections.txt (with props) >This would be good to have too: segmentHeading: HISTORY OF PRESENT ILLNESS: There is a field called Segment.preferredText. Which should display the first text column in the mappings file… Thanks, Pei From: digital paula [mailto:[email protected]] Sent: Wednesday, December 04, 2013 8:59 PM To: [email protected]<mailto:[email protected]> Subject: RE: cTAKES Sectionizer: how to integrate it with clinical pipeline - Solved Pei, Okay, the sectionizer is now integrated in the clinical pipeline and I did some preliminary testing to confirm. I added the CDASegmentAnnotator lines that you stated to the Aggregate Descriptor and commented the simple annotator in the flow. In addition, I also had to comment out this in order for the Aggregate descriptor to save with no error: <!-- <configurationParameter> <name>SegmentID</name> <description/> <type>String</type> <multiValued>false</multiValued> <mandatory>false</mandatory> <overrides> <parameter>SimpleSegmentAnnotator/SegmentID</parameter> </overrides> </configurationParameter> --> I didn't see it in the trunk so I manually added the text file ccda_sections.txt taken from the sandbox. I added it under src/main/resources in ctakes-core: org/apache/ctakes/core/sections/ccda_sections.txt I tested on a few narratives and I'm attaching what returned using CVD tool for one of them. The segmentID was populated with segmentID: 1.3.6.1.4.1.19376.1.5.3.1.3.4. I looked in the ccda_sections.txt file and this was it: 1.3.6.1.4.1.19376.1.5.3.1.3.4,10164-2,HISTORY OF PRESENT ILLNESS,brief history of physical illness,history of present illness,history of the present illness I looked back in the narrative and the heading was: HISTORY OF PRESENT ILLNESS: The patient..... I just tested on a few narratives and though that hardly constitutes testing because I need to resolve a more urgent issue for my research but will return to this for full testing entailing the application to all of my narratives. However, from a preliminary perspective, it looks good....only thing I'd like to see is the actual text as well for the segment heading as another feature. For example what displays is this: segmentID: 1.3.6.1.4.1.19376.1.5.3.1.3.4 This would be good to have too: segmentHeading: HISTORY OF PRESENT ILLNESS: Thanks. Regards, Paula > From: [email protected]<mailto:[email protected]> > To: [email protected]<mailto:[email protected]> > Subject: RE: cTAKES Sectionizer: how to integrate it with clinical pipeline > Date: Tue, 3 Dec 2013 20:38:22 +0000 > > Paula, > I moved the sectionizer to trunk now and added the xml descriptor for it. > > In your Aggregate Descriptor, just add: > <delegateAnalysisEngine key="CDASegmentAnnotator"> > <import > location="../../../ctakes-core/desc/analysis_engine/CDASegmentAnnotator.xml"/> > </delegateAnalysisEngine> > . > <node>CDASegmentAnnotator</node> > > If you would like to see it wired together via uimaFIT, check out the test > case: > ctakes-core/src/test/java/org/apache/ctakes/core/ae/TestCDASegmentAnnotator.java > > Hope that helps. > It might be even worthwhile defaulting to this instead of the SimpleSegment > (since simple segment does nothing more than span the entire document...) > --Pei > > > > From: digital paula > [mailto:[email protected]]<mailto:[mailto:[email protected]]> > Sent: Tuesday, December 03, 2013 1:51 PM > To: [email protected]<mailto:[email protected]> > Subject: cTAKES Sectionizer: how to integrate it with clinical pipeline > > Hi Pei, > > Last week we discussed briefly the sectionizer and now that I have it loaded > successfully I just need to integrate it in the clinical pipeline. > > The sectionizer doesn't have a desc folder with associated XML descriptor and > I understand that things are moving towards UIMAfit so that's probably the > reason why it doesn't. Can you provide some guidance on what you'd recommend > for testing the sectionizer? That is, should I just create the XML > Descriptor using one of the reference materials from the UIMA website for > creating descriptors or would you recommend using UIMAfit? If the latter, > can you provide assistance of how to integrate the sectionizer into the > AggregatePlaintext AE using UIMAfit. > > Thanks. > > Regards, > Paula
