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From Chase Master <chasemast...@gmail.com>
Subject Re: Viewing MedicationMentions from drug-ner in Annotation Viewer
Date Wed, 21 Aug 2013 16:11:26 GMT
Thanks, using the type system xml instead of the AE xml helped!


On Wed, Aug 21, 2013 at 10:45 AM, Chen, Pei
<Pei.Chen@childrens.harvard.edu>wrote:

> 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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