Thanks, using the type system xml instead of the AE xml helped!
On Wed, Aug 21, 2013 at 10:45 AM, Chen, Pei <[email protected]>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:[email protected]] > Sent: Wednesday, August 21, 2013 9:28 AM > To: [email protected] > 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 <[email protected] > <mailto:[email protected]>> 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" <[email protected] > <mailto:[email protected]>> 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 > >
