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Posted to dev@ctakes.apache.org by Chase Master <ch...@gmail.com> on 2013/08/20 20:09:54 UTC
Viewing MedicationMentions from drug-ner in Annotation Viewer
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
Re: Viewing MedicationMentions from drug-ner in Annotation Viewer
Posted by Chase Master <ch...@gmail.com>.
Thanks, using the type system xml instead of the AE xml helped!
On Wed, Aug 21, 2013 at 10:45 AM, Chen, Pei
<Pe...@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
> <ma...@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
> <ma...@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
>
>
RE: Viewing MedicationMentions from drug-ner in Annotation Viewer
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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 <Pe...@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" <ch...@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
Re: Viewing MedicationMentions from drug-ner in Annotation Viewer
Posted by Chase Master <ch...@gmail.com>.
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
<Pe...@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" <ch...@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
>
Re: Viewing MedicationMentions from drug-ner in Annotation Viewer
Posted by "Chen, Pei" <Pe...@childrens.harvard.edu>.
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" <ch...@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