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From "Wu, Stephen T., Ph.D." <Wu.Step...@mayo.edu>
Subject Type System updates
Date Thu, 17 Jul 2014 19:30:01 GMT
The type system needs some updating.  Here are some reasons:

1. The refsem and textsem namespaces were created to reflect the Secondary Use Clinical Element
Models (CEMs) defined in the SHARP project.  However, later modification to those models are
not reflected in the cTAKES type system.

2. Wendy Chapman, Melissa Tharp, et al (CC'ed here) have done some quantitative studies showing
that physicians do not easily categorize their named entities of interest into cTAKES types.
 For example, even if we could pick up values (as James mentioned, we don't pick up many),
how would you categorize an Apgar score?  That kind of thing is not exactly a Procedure, Lab,
or SignSymptom -- at least, physicians don't seem to think so.

3. We have been using the type system for a while and it might be due time for some ground-up
modifications (though I do think this is more of an ongoing task).

The courses of action we can take are aligned somewhat to these different reasons.

I. Try to reconcile the CEMs with the Type System.  Here is a diff, put together by Melissa
I feel like this will be quite complicated, especially given the differences between Assertion
and SignSymptom.  Also, if we add everything from the CEMs, that significantly adds to the
Modifiers that we have to create to house those types.  Each attribute of a CEM may require
its own processing and evaluation (i.e., you might need a dedicated analysis engine just to
discover DiseaseDisorder:severity), but in practice there may be too many options of types
and attributes.

II. Follow the work being done on physician-validated types.  Melissa might be able to put
together another document with the differences between their resulting types (Schema Ontology)
and our Type System.  We could then use this to update the types with what physicians are
actually looking for.

III. Solicit user/developer-initiated changes, to be made at the same time as one or both
of the above.

What does everyone think?

P.S. Please use swu@apache.org or stw4@alumni.duke.edu for future correspondence!
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