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From "John Green" <john.travis.gr...@gmail.com>
Subject Re: Procedure
Date Thu, 17 Jul 2014 18:39:53 GMT
Hey, thanks! 


JG
—
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On Thu, Jul 17, 2014 at 2:37 PM, Bruce Tietjen
<bruce.tietjen@perfectsearchcorp.com> wrote:

> 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.
>  [image: IMAT Solutions] <http://imatsolutions.com>
>  Bruce Tietjen
> Senior Software Engineer
> [image: Mobile:] 801.634.1547
> bruce.tietjen@imatsolutions.com
> 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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