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From "Chen, Pei" <Pei.C...@childrens.harvard.edu>
Subject Re: Viewing MedicationMentions from drug-ner in Annotation Viewer
Date Tue, 20 Aug 2013 21:59:24 GMT
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> 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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