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From David Kincaid <kincaid.d...@gmail.com>
Subject Vital signs annotation
Date Wed, 26 Nov 2014 17:36:54 GMT
I'm sure I'm not the first one to struggle to understand this, but I was
unable to find an explanation in the mailing list archives. I am wondering
about how to represent the values of vital signs (such as temperature,
pulse, blood pressure, etc) when annotating some text.

For example, if I have the following text:

Temperature: 98.8, pulse: 65, bp 120/80

and I'd like to identify the values associated with each so I can pull them
out later into structured data fields somewhere else. Right now running
this through the cTAKES clinical pipeline I get the following relevant

NumToken: 98.8
NumToken: 65
NumToken: 120
NumToken: 80
MeasurementAnnotation: 120/80
SignSymptomMention (with UMLS CUI C0005823): bp

I'm disappointed that it didn't annotate "temperature" or "pulse", but
that's probably a configuration problem on my side.

So what I'd like to do now is to have the 120/80 value be annotated as as
blood pressure vital sign. Do I do that using SignSymptom type? If so,
where does the value 120/80 go? Does it go into the "mentions" array? That
doesn't seem quite right for some reason.

My idea was to create a new annotator that looks at the combination of
SignSymptomMention and NumToken (or even better MeasurementAnnotation) and
creates a representation of the sign with its value and other pertinent
attributes in the CAS (probably as a SignSymptom type).

How do others do this?



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