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From Steven Bethard <steven.beth...@Colorado.EDU>
Subject Re: SHARPKnowtatorXMLReader
Date Thu, 13 Dec 2012 10:24:11 GMT
On Dec 12, 2012, at 7:43 PM, "Wu, Stephen T., Ph.D." <Wu.Stephen@mayo.edu> wrote:
> I've been looking at your (Steve B's) code, and it seems like it's been
> written so that everything hinges on Annotations subtypes being created for
> everything.

Yep, that's right. To train a severity modifier classifier, for example, we need some Annotation
sub-type that marks the spans of severity modifiers.

> Are these type system barriers the main problems with
> connecting relations and attributes to their corresponding NEs?

That's one of the big problems, yes.

>  (There is a
> layer that does not seem to be happening -- namely, that the values of NE
> attributes/relations don't get populated.  I don't fully understand the
> DelayedFeatures but assume that they would work if the types were set?)

This is the other big problem. Basically, we need to be able to say something like:

diseaseDisorderMention.setBodySide(bodySideMention)

And so on, for all the mention types. Once such methods exist, I can update the DelayedFeature
implementations to actually set those features.

Ideally, we'd set the inheritance hierarchy up correctly so that all Mentions that have a
bodySide feature (DiseaseDisorder, Procedure, SignSymptom) have some common superclass, all
Mentions that have a course (DiseaseDisorder, SignSymptom) have some common superclass, etc.
If this is not possible, we can get around it with instanceof and casting, but if it is possible,
it would be great.

On Dec 12, 2012, at 7:57 PM, "Chen, Pei" <Pei.Chen@childrens.harvard.edu> wrote:
> I would suggest the "Apache way" here? : Open a Jira, Discuss on ctakes-dev as appropriate
(call a Vote if there are contentions), Commit the code.
> Any committers should have access to make the changes to the code.

I've added some comments to the issue (https://issues.apache.org/jira/browse/CTAKES-57) as
well. Stephen, let me know if you plan to make these changes or if you'd like me to.

Thanks,

Steve
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