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From Pei Chen <chen...@apache.org>
Subject Re: specificity in selecting EntityMentions when using AggregatePlaintextUMLSProcessor
Date Wed, 04 Sep 2013 01:55:28 GMT
It has the correct parse (POS, chunks, and lookupwindow)- but some of
the terms do not exist in SNOMED-
CIN 2 - Cervical intraepithelial neoplasia 2
[A3002688/SNOMEDCT/SY/285838002] exists but not CIN II.
CIN III [A3333965/SNOMEDCT/SY/20365006] also exists that's why it was
able to perform the lookup successfully.
Note that CIN II synonyms do exist in other umls thersauses such as
MEDCIN, CCPSS though.  However, the bundled cTAKES dictionaries only


On Tue, Sep 3, 2013 at 9:44 PM, Miller, Timothy
<Timothy.Miller@childrens.harvard.edu> wrote:
> That is a good question, Ted!
> I tried it with a simple context: "The patient has a CIN III." I'm not
> sure if that is a correct context but I was able to duplicate your
> findings. (Finds a CUI for CIN III but not if you change it to CIN II)
> My first thought was that it is the chunker. But the chunker seems to
> get it right, as CIN II and CIN III are both called NPs, and similarly
> the LookupWindowAnnotator handles them both identically. So that
> suggests it is a problem with the actual lookup of the tokens in the
> LookupWindow.
> That's all I can do for now but maybe someone else who knows more about
> its behavior offhand will have an idea.
> Tim
> On 09/03/2013 08:24 PM, Assur, Ted wrote:
>> I'm trying to understand what would prevent the AggregatePlaintextUMLSProcessor AE
from correctly parsing specific problems that are defined in the UMLS version used by cTAKES.
>> For example,
>> CIN (Cervical Intraepithelial Neoplasia) in its general usage is parsed out as UMLS
CUI C0206708.
>> CIN comes in 3 grades, 1, 2 and 3. Sometimes this is reported with Roman Numerals,
I,II, and III.
>> cTAKES correctly identifies "CIN 3" and "CIN III" with UMLS CUI C0851140: "Carcinoma
in situ of uterine cervix."
>> However, I cannot get it to recognize CIN 1, CIN I, CIN 2, or CIN II as their correct
concepts, "Cervical intraepithelial neoplasia grade 1" and "Cervical intraepithelial neoplasia
grade 2" respectively.
>> Is there a way to tune the detection of UMLS concepts?
>> --------------------------------------------
>> Ted Assur
>> IT Solutions Architect for Cancer Research
>> Providence Health & Services
>> ted.assur@providence.org
>> 503-215-6476
>> Crede, ut intelligas.
>> Intellego, ut credam.
>>   ________________________________
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