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From Steven Bethard <steven.beth...@gmail.com>
Subject Re: CEM Template Question
Date Fri, 23 Aug 2013 13:05:09 GMT
On Thu, Aug 22, 2013 at 10:03 AM, Wu, Stephen T., Ph.D.
<Wu.Stephen@mayo.edu> wrote:
> Yeah, Steve is right -- we did this to mirror the Knowtator annotation
> schema.  Removing the relation between them would make it difficult to
> find and account for relation attributes.
>
> I think there's a pretty convincing argument for relations being somewhat
> "supporting" annotations.  Coreference and all other relations would
> essentially help you fill in your attribute values (e.g.,
> mention.setbodyLocation()).  I think this ends up being cleaner overall,
> since an end user of the CAS then has the ability to look at Mentions
> without looking at Relations.
>
> So I think I'm a +1.  There are only a few relation-valued attributes for
> each mention, so I expect changes would be fairly local within the
> relation-extractor project.
>
> What do you think about the refsem types -- e.g., should the attributes
> within DiseaseDisorder changed, similar to how we plan to change
> DiseaseDisorderMention?

I would say yes. I think we want these types to parallel each other as
much as possible.

Steve

>
> stephen
>
>
> On 8/19/13 7:40 PM, "Chen, Pei" <Pei.Chen@childrens.harvard.edu> wrote:
>
>>That's a good point.
> >From a pragmatic perspective, my vote would be to have the
>>XMention.getBodyLocation() return a AnatomicalSiteMention and similar for
>>Severity etc.
>>If the relation was negated (there was no relation), then I think the CEM
>>template filler can just not create the relation.
>>For the extremely rare cases where they need to differentiate the null vs
>>explicit negated case, they can still iterate though the
>>BinaryTextRelations because we didn't lose the data.
>>
>>--Pei
>>________________________________________
>>From: Steven Bethard [steven.bethard@gmail.com]
>>Sent: Monday, August 19, 2013 2:12 PM
>>To: dev@ctakes.apache.org
>>Subject: Re: CEM Template Question
>>
>>On Fri, Aug 16, 2013 at 8:29 PM, Pei Chen <chenpei@apache.org> wrote:
>>> Hi James/Steven,
>>> In the common type system/template fillers, do you recall why we stored
>>>the
>>> TextRelation instead of the resolved annotation?
>>>
>>> For example, in SignSymptomMention, getBodyLocation() returns
>>> LocationOfTextRelation.
>>> So in order to actually get the AnatomicalSiteMention, you would have to
>>> look inside LocationOfTextRelation arg1 or arg2.
>>
>>Yeah, I really didn't like this either, but this is what's in the
>>actual Knowtator data. The one argument I've heard for it is that the
>>LocationOfTextRelation could be negated, even when the
>>AnatomicalSiteMention was not. I believe the idea would be to
>>distinguish between:
>>
>>* The lesion was not on the left lung
>>* There was no lesion on the left lung
>>
>>where the former asserts that there was a lesion but negates the
>>location, and the latter asserts the lack of a lesion. To support this
>>kind of thing, either getBodyLocation() has to return a
>>LocationOfTextRelation with an appropriate polarity attribute, of
>>there has to be some other mechanism for specifying the polarity, etc.
>>of the body location relation.
>>
>>All that said, this was just got said to me once or twice. I have no
>>idea if the annotators even annotated this way or not. If they didn't,
>>I agree that the LocationOfTextRelation as the bodyLocation feels
>>super clunky and it would be great to fix that.
>>
>>Steve
>>
>>On Fri, Aug 16, 2013 at 8:29 PM, Pei Chen <chenpei@apache.org> wrote:
>>> Hi James/Steven,
>>> In the common type system/template fillers, do you recall why we stored
>>>the
>>> TextRelation instead of the resolved annotation?
>>>
>>> For example, in SignSymptomMention, getBodyLocation() returns
>>> LocationOfTextRelation.
>>> So in order to actually get the AnatomicalSiteMention, you would have to
>>> look inside LocationOfTextRelation arg1 or arg2.
>>>
>>> I think it be more intuitive and simpler for consumers of the CEM's to
>>>just
>>> store the AnatomicalSiteMention?  Is there a use case I am missing where
>>> someone would want something different than the
>>> SignSymptomMention.getBodyLocation() other than the actual
>>> AnatomicalSiteMention?
>>>
>>> --Pei
>

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