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Posted to user@ctakes.apache.org by Vlad Valtchinov <vl...@gmail.com> on 2014/09/19 19:14:46 UTC

process only IMPRESSION section of a note

Hi everyone-

 

can ctakes process only a predefined section of a document (radiology
report), for example the last section in the reports, IMPRESSION? Of course,
one can go and parse out this section only in a new document and do it this
way but with millions of such notes the cleaner way would be to instruct
ctakes to only process a specific section.

 

Thanks ,

vlad

Re: process only IMPRESSION section of a note

Posted by Pei Chen <ch...@apache.org>.

Vlad,
cTAKES has a sectionizer component.
Depending on your use case, one may consider something like:
1) If you wish to have cTAKES to completely ignore all sections except
IMPRESSION, it can be done as a preprocessing step.  (either removed
beforehand, or modify all of the annotators to support only process
certain sections.  (not all components support this by config by
default though).
2) Each IdentifiedAnnotation has a Section attribute associated with
it (I think it's .getSection() IIRC).  So you can also do it as a post
filtering.
Pros and Con's to both.

On Fri, Sep 19, 2014 at 1:14 PM, Vlad Valtchinov
<vl...@gmail.com> wrote:
> Hi everyone-
>
>
>
> can ctakes process only a predefined section of a document (radiology
> report), for example the last section in the reports, IMPRESSION? Of course,
> one can go and parse out this section only in a new document and do it this
> way but with millions of such notes the cleaner way would be to instruct
> ctakes to only process a specific section.
>
>
>
> Thanks ,
>
> vlad
>
>

Re: process only IMPRESSION section of a note

Posted by "Miller, Timothy" <Ti...@childrens.harvard.edu>.

Vlad,
The most natural way to do this would be to create your own version of SegmentAnnotator. Most cTAKES components iterate over Segment annotations and process text in each segment. So if you create an annotator that annotates the IMPRESSION section as the only segment that will be the only text that gets processed by subsequent annotators.

Tim

On 09/19/2014 01:15 PM, Vlad Valtchinov wrote:
Hi everyone-

can ctakes process only a predefined section of a document (radiology report), for example the last section in the reports, IMPRESSION? Of course, one can go and parse out this section only in a new document and do it this way but with millions of such notes the cleaner way would be to instruct ctakes to only process a specific section.

Thanks ,
vlad