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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject RE: Viewing MedicationMentions from drug-ner in Annotation Viewer
Date Wed, 21 Aug 2013 15:45:00 GMT
The Type System file is available at:
http://svn.apache.org/repos/asf/ctakes/trunk/ctakes-type-system/src/main/resources/org/apache/ctakes/typesystem/types/TypeSystem.xml
Have you tried editing the TypeSystemStyleMap.xml (the annotationViewer should have created
one), maybe it's just missing from the map.
I do not use the viewer too much, but it could be something weird as I'm able to see the different
types of the sample_note.xml in an html format.
--Pei


From: Chase Master [mailto:chasemaster9@gmail.com]
Sent: Wednesday, August 21, 2013 9:28 AM
To: dev@ctakes.apache.org
Subject: Re: Viewing MedicationMentions from drug-ner in Annotation Viewer

I loaded the AE descriptor file...I've attached both my output and this descriptor.  Not sure
where to find the consolidated type system file...
Thanks

On Tue, Aug 20, 2013 at 4:59 PM, Chen, Pei <Pei.Chen@childrens.harvard.edu<mailto:Pei.Chen@childrens.harvard.edu>>
wrote:
That is strange especially if you see the types in your output xml. Did you load the consolidated
type system file to the annotation viewer?  If possible, could you send the typesystem xml
and output xml used? I'll see if I can recreate it...

Sent from my iPhone

On Aug 20, 2013, at 2:10 PM, "Chase Master" <chasemaster9@gmail.com<mailto:chasemaster9@gmail.com>>
wrote:

> Hi,
>
> To get a feel for how a module works, I like viewing the annotations that
> it outputs with UIMA's AnnotationViewer.  I'm wondering why for the
> drug-ner module, you can see MeasurementAnnotations (e.g. 80mg), but you
> can't see MedicationMentions, MedicationStrengths, etc. in the GUI even
> though these annotations are also in my output xml file, and also contain a
> text span?  Actually, on second glance, it looks like for the
> "MedicationStrengthModifiers" the span is not set (begin=0, end=0).  But it
> is valid for the MedicationMentions (e.g. begin=269, end=282).  These
> annotations appear to be part of the typesystem, and I'm pointing the
> Annotation Viewer to the drug-ner pipeline I used...
>
> Thanks


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