Vital signs annotation

[David Kincaid <ki...@gmail.com>]

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
annotations:

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?

Thanks,

Dave

Re: Vital signs annotation

[Sangram <sa...@figmd.com>]

David Kincaid <ki...@...> writes:

> 
> 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 
annotations:
> 
> 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?
> 
> Thanks,
> 
> Dave
> 
> 


The same requirement I am looking for... could you please do favor and pass 
on the resolution if you come across any.