ctakes-dev mailing list archives

Site index · List index
Message view « Date » · « Thread »
Top « Date » · « Thread »
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"
,etc.
It should also be able to identify "CIN 2" as there should be an exact
match in SNOMEDCT: (CIN 2 - Cervical intraepithelial neoplasia 2
[A3002688/SNOMEDCT/SY/285838002]
Please see attached xml output.

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

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
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.
>
>
>
>
>   ________________________________
>
> This message is intended for the sole use of the addressee, and may contain information
that is privileged, confidential and exempt from disclosure under applicable law. If you are
not the addressee you are hereby notified that you may not use, copy, disclose, or distribute
to anyone the message or any information contained in the message. If you have received this
message in error, please immediately advise the sender by reply email and delete this message.

Mime
View raw message