SHARPKnowtatorXMLReader

["Wu, Stephen T., Ph.D." <Wu...@mayo.edu>]

So back to the issue of the reading in Knowtator XML data...

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

  1. We haven't created the LabMention, ProcedureMention,
AnatomicalSiteMention, DiseaseDisorderMention, and SignSymptomMention types
that we had planned to, yet!  Or at least, they're not checked in.

  2. We also haven't created comprehensive Annotations for modifiers.

Who has the authority to add these, as appears to have been agreed upon by
everyone?  I am not clear on the process for managing the type system these
days...  
 - SHARP SDG (in original SHARP plans -- though I'm not a member)?
 - Apache ctakes-dev (as most other stuff these days)?
 - Me and James (what it's mostly been for the type system thus far)?

E.g., could Steve B. or anyone else on this list add them, esp. since
they've been discussed?  I could do it too, but it seems like
relation/attribute functionality in SHARPKnowtatorXMLReader has been held up
a long time because we're confused about who can change the type system.

stephen

Re: SHARPKnowtatorXMLReader

[Steven Bethard <st...@Colorado.EDU>]

On Dec 12, 2012, at 7:43 PM, "Wu, Stephen T., Ph.D." <Wu...@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" <Pe...@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

RE: SHARPKnowtatorXMLReader

["Chen, Pei" <Pe...@childrens.harvard.edu>]

> Who has the authority to add these, as appears to have been agreed upon
> by everyone?  I am not clear on the process for managing the type system
> these days...
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.

--Pei


> -----Original Message-----
> From: Wu, Stephen T., Ph.D. [mailto:Wu.Stephen@mayo.edu]
> Sent: Wednesday, December 12, 2012 1:45 PM
> To: ctakes-dev@incubator.apache.org
> Subject: SHARPKnowtatorXMLReader
> 
> So back to the issue of the reading in Knowtator XML data...
> 
> 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.  Are these type system barriers the main problems with
> connecting relations and attributes to their corresponding NEs?  (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?)
> 
>   1. We haven't created the LabMention, ProcedureMention,
> AnatomicalSiteMention, DiseaseDisorderMention, and
> SignSymptomMention types that we had planned to, yet!  Or at least, they're
> not checked in.
> 
>   2. We also haven't created comprehensive Annotations for modifiers.
> 
> Who has the authority to add these, as appears to have been agreed upon
> by everyone?  I am not clear on the process for managing the type system
> these days...
>  - SHARP SDG (in original SHARP plans -- though I'm not a member)?
>  - Apache ctakes-dev (as most other stuff these days)?
>  - Me and James (what it's mostly been for the type system thus far)?
> 
> E.g., could Steve B. or anyone else on this list add them, esp. since they've
> been discussed?  I could do it too, but it seems like relation/attribute
> functionality in SHARPKnowtatorXMLReader has been held up a long time
> because we're confused about who can change the type system.
> 
> stephen