Hey, thanks!
JG — Sent from Mailbox for iPhone On Thu, Jul 17, 2014 at 2:37 PM, Bruce Tietjen <bruce.tiet...@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.tiet...@imatsolutions.com > On Thu, Jul 17, 2014 at 11:57 AM, John Green <john.travis.gr...@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.ja...@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.gr...@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.ja...@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.gr...@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 >> >> >>
