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From Pei Chen <chen...@apache.org>
Subject Re: specificity in selecting EntityMentions when using AggregatePlaintextUMLSProcessor
Date Wed, 04 Sep 2013 01:43:42 GMT
Hi Ted,
Detecting the stage/grade and other attributes and asserting those
relationships to the cancer aside (That's probably a separate
discussion)-  But in your example, since there are distinct SNOMEDCT
concepts and direct matches, it was able to identify "Cervical
intraepithelial neoplasia grade 1"
cui = "C0349458"
code = "285836003"
as well as "Cervical intraepithelial neoplasia"
cui = "C0206708"
code = "285636001"
It should also be able to identify "CIN 2" as there should be an exact
match in SNOMEDCT: (CIN 2 - Cervical intraepithelial neoplasia 2
Please see attached xml output.

I am using out of the box AggregatePlaintextUMLSProcessor from the 3.1RC3

On Tue, Sep 3, 2013 at 8:24 PM, Assur, Ted
<Theodore.Assur@providence.org> 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
> 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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