The order you mentioned in your previous email had been "pulsatile abdominal
mass" for both what is in UMLS and what was in the text being annotated, which
is why I was asking about the ordering.
Given that I now know the text you were annotating did have a different word
order than what is in umls, and seeing exactly what those orderings were, that
explains why it was not being picked up.
A quirk/feature of cTAKES (current) dictionary lookup (as opposed to the newer
one called lookup-2) is that the first word must be first, but in a multi (>2)
word entry, the order of the other words doesn't matter.
So for example, with "abdominal pulsatile mass" in the dictionary, both of
these should get annotated with the same cui
abdominal pulsatile mass
abdominal mass pulsatile
but this will not get an annotation for that CUI
pulsatile abdominal mass
unless that ordering is also in the dictionary.
As far as heart rate and temperature, whether they are annotated as procedures
all depends on if they show up in the UMLS with the semantic types used by
cTAKES.
To check those, I would do this
- Open the UMLS terminology services Metathesaurus Browser app
https://uts.nlm.nih.gov/home.html
Applications->UTS Metathesaurus Browser
- input the text of interest into the box in the left pane, and click Go
- select the CUI that looks hopeful
- the pane on the right will fill in with details about that Concept, including
the semantic all the Atoms.
- look at the Semantic Types in the pane on the right
- if not a semantic type that cTAKES annotates, select a different CUI
- Once found a CUI with a semantic type cTAKES annotates, if the text of the
UMLS Concept itself is not exactly what I was looking for, look at all the
Atoms, and see if the text I was looking for appears with SNOMED_CT, NCI, MSH,
or ICD9CM.
Note that cTAKES also uses normalized forms of the words in the text being
processed, so if the input text were "lymph nodes" it would match a
hypothetical dictionary entry of "lymph node".
Also note that intervening words can be OK, up to a limit, but all words within
the term must appear within a single LookupWindow.
Hope that is helpful
-- James
-----Original Message-----
From: John Green [mailto:[email protected]]
Sent: Thursday, July 17, 2014 12:57 PM
To: [email protected]
Cc: [email protected]
Subject: RE: Procedure
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. <[email protected]>
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:[email protected]]
> Sent: Thursday, July 17, 2014 8:04 AM
> To: [email protected]
> 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. <[email protected]>
> 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:[email protected]]
>> Sent: Wednesday, July 16, 2014 2:01 PM
>> To: [email protected]
>> Subject: Procedure
>>
>> Is there a generally accepted procedure for identifying why an annotation
>> wasnt made?
>>
>> JG
>>
