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From Nick Nikandish <snika...@emerginghealthit.com>
Subject RE: Ctakes to process 5000K recoreds
Date Tue, 09 Sep 2014 19:11:49 GMT
I am only interested in medications names so I use cTakes for that sole purpose for now(the
future plan is to use other parts of cTakes) . I  don't believe I am getting any annotation
If I only want to use identify the medication/antibiotics name in a text like this:
  Urine culture                                                       MOS Source/Body site
         Not Indicated . . Culture results . >100,000col/ml Escherichia coli          
               Final  ID . . E.coli Ampicillin              S Ampicillin/sulbactam    S Cefazolin
              S Ciprofloxacin           S Gentamicin              S Nitrofurantoin       
  S SXT                     S

What is the minimum annotator flow that I have to use? I tried to take out some of the mentioned
flow members but it didn't work.


-----Original Message-----
From: Masanz, James J. [mailto:Masanz.James@mayo.edu] 
Sent: Tuesday, September 09, 2014 3:05 PM
To: 'dev@ctakes.apache.org'
Subject: RE: Ctakes to process 5000K recoreds

I suspect that when you take out simple segment annotated, nothing is getting processed, and
that is why it appears so fast. At least some of the annotators loop through the list of sections/segments,
which is why there is a simple segment annotator - so that there is at least one section/segment
identified. Are you getting any annotations at all?

-----Original Message-----
From: Nick Nikandish [mailto:snikandi@emerginghealthit.com] 
Sent: Tuesday, September 09, 2014 2:02 PM
To: dev@ctakes.apache.org
Subject: RE: Ctakes to process 5000K recoreds

I need the name of the medications for the application that I wrote and uses ctakes.....so
I cache the medication in DictionaryLookupAnnotator(in performLookup()) and use them in my
program but when I have SimpleSegementAnnotator it just takes forever. After taking SimpleSegementAnnotator
out, no medication name in DictionaryLookupAnnotator is returned in the code. So I was wondering
if there was a way that I could eliminate SimpleSegementAnnotator but still be  able to get
the medications name in that class?


-----Original Message-----
From: Pei Chen [mailto:chenpei@apache.org] 
Sent: Tuesday, September 09, 2014 2:54 PM
To: dev@ctakes.apache.org
Subject: Re: Ctakes to process 5000K recoreds

When you mean no medication is being annotated, I presume you mean the medication attributes
(i.e. dosage, frequency, etc.) are not being annotated?  I think the DrugNER needs a list
of section names in the config; I think it includes SIMPLE_SEGMENT.  I am very surprised that
SimpleSegementAnnotator is the bottle neck though; all it does is assume the entire document
is a single section called SIMPLE_SEGMENT.
Have you tried commenting out the DependencyParser if you're not using those features.


On Tue, Sep 9, 2014 at 2:45 PM, Nick Nikandish <snikandi@emerginghealthit.com> wrote:
> Hi there,
> I am using Ctakes to process 5000K free text  records  where each record has several
> This is the fixed flow that it goes through:
>                                                                <node>SimpleSegmentAnnotator</node>
>                                                                 <node>SentenceDetectorAnnotator</node>
>                                                                 <node>TokenizerAnnotator</node>
>                                                                 <node>LvgAnnotator</node>
>                                                                 <node>ContextDependentTokenizerAnnotator</node>
>                                                                 <node>POSTagger</node>
>                                                                 <node>Chunker</node>
>                                                                 <node>LookupWindowAnnotator</node>
>                                                                 <node>DictionaryLookupAnnotatorDB</node>
>                                                                 <node>DependencyParser</node>
>                                                                 <node>AssertionAnnotator</node>
> <node>ExtractionPrepAnnotator</node>
> But it takes very very long time to process that many data( maybe a week or so) when
I use SimpleSegmentAnnotator.  By eliminating SimpleSegmentAnnotator the process is very fast
but no medication is being anotated.  Do you guys have any suggestion?
> Thanks,
> Nick
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