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From "John Green" <john.travis.gr...@gmail.com>
Subject RE: Procedure
Date Thu, 17 Jul 2014 17:57:02 GMT
I didnt see how it appeared in dictionary, I just looked at the cui in umls, which has it as
abdominal pulsatile mass, which isnt the same order as the text I annotated in ctakes (pulsatile
abdominal mass); but if im wrong great, it does raise the question even more why if it was
in the lookup window and in the dictionary that it was only annotated as abdominal mass.

Apropos temperature and heart rate, the results of these are measurements right? But it seems
also that they should be procedures in the sense that you perform a physical manipulation
on a pt. If I were checking notes for the presence of whether or not someone checked vitals
vs obtaining the measurements, this seems within the current use case, but Im so often wrong
here being so new... 


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On Thu, Jul 17, 2014 at 1:44 PM, Masanz, James J. <Masanz.James@mayo.edu>

> In general cTAKES doesn't pick up things with values, such as weight, height, lab values,
temperature, with the exception that the drug ner pipeline can pick up medication related
values such as dose, strength, etc.
> cTAKES does pick up a few things as MeasurementAnnotation just by pattern, but doesn't
associate those with a named entity that has a cui.
> The example of "pulsatile abdominal mass" listed the same 3 words in the same order for
the dictionary entry and the text that was processed, so I'm not clear what you meant about
word order.
> -----Original Message-----
> From: John Green [mailto:john.travis.green@gmail.com] 
> Sent: Thursday, July 17, 2014 8:04 AM
> To: dev@ctakes.apache.org
> Subject: Re: Procedure
> General so that I dont keep generating work for others :-)
> Specifically: Temperature wasnt annotated, neither was Heart rate, for
> example.
> different but related: it picked up "abdominal mass" (C0000734) but not
> "pulsatile abdominal mass" (C0266835) when given "pulsatile abdominal
> mass". I understand that this may be expected given the word order. If it
> wasnt, then the concern, of course, is that by clinical intuition abdominal
> mass isnt very specific and one wouldnt jump to thinking AAA. However,
> pulsatile abdominal mass you would immediately think AAA. While this delta
> is fairly well reflected in ytex's semantic similarity measure
> (particularly LCH) with the distance being 0.84 and 0.64 for abdominal mass
> to pulsatile abdominal mass and Abdominal Aortic Aneurysm (C0162871)
> respectively.
> Pulsatile abdominal mass was in the lookup window.
> JG
> On Wed, Jul 16, 2014 at 3:07 PM, Masanz, James J. <Masanz.James@mayo.edu>
> wrote:
>> It depends on the type of annotation.
>> Some are rule-based. Some are machine-learning based (models).  Some are
>> dictionary dependent.  And some are based on annotations earlier in the
>> pipeline, and so looking at the part of speech tags within the tokens, for
>> example, can explain which chunk something appears in, which can explain
>> why something might not have been annotated as a DiseaseDisorderMention,
>> for example.
>> Are you asking a general question or is there a specific type of
>> annotation you are most interested in.
>> -----Original Message-----
>> From: John Green [mailto:john.travis.green@gmail.com]
>> Sent: Wednesday, July 16, 2014 2:01 PM
>> To: dev@ctakes.apache.org
>> Subject: Procedure
>> Is there a generally accepted procedure for identifying why an annotation
>> wasnt made?
>> JG
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