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From "John Green" <john.travis.gr...@gmail.com>
Subject Re: Type System updates
Date Thu, 17 Jul 2014 20:27:35 GMT
As a clinician Id really like to see the types that Melissa has elicited from physicians.

By the by: Id call apgar, or duke, or has bled score, or chads vasc, or childs criteria, or
anything else like them risk classifiers or prognosticators or decision models or something
like that (the line between is fuzzy sometimes).


On Thu, Jul 17, 2014 at 3:30 PM, Wu, Stephen T., Ph.D.
<Wu.Stephen@mayo.edu> wrote:

> 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
>         http://bit.ly/WkqCPa
> 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?
> stephen
> P.S. Please use swu@apache.org or stw4@alumni.duke.edu for future correspondence!
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