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 Tharp:
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 s...@apache.org or s...@alumni.duke.edu for future
correspondence!
