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From Bruce Tietjen <bruce.tiet...@perfectsearchcorp.com>
Subject Re: Procedure
Date Thu, 17 Jul 2014 18:36:48 GMT
I believe it wouldn't be picked up because the first word dictionary lookup
algorithm only does lookups by first word as it progresses through the
words in the lookup window.

>From the lookup window, it would do:

pulsatile abdominal mass --> lookup word 'pulsatile'
abdominal mass --> lookup word 'abdominal'
mass --> lookup word 'mass


Since the dictionary entry is 'Abdominal pulsatile mass', the lookup key is
'Abdominal'.  the lookup for 'pulstile' would not find it.
When it does the 'abdominal mass' lookup, the word 'pulsatile' has already
been dropped and so it will not match the full word matching for this entry.





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 Bruce Tietjen
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On Thu, Jul 17, 2014 at 11:57 AM, John Green <john.travis.green@gmail.com>
wrote:

> 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...
>
>
>
>
> JG
>
>
>
>
>
>
>
> —
> Sent from Mailbox for iPhone
>
> On Thu, Jul 17, 2014 at 1:44 PM, Masanz, James J. <Masanz.James@mayo.edu>
> wrote:
>
> > 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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