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From Pei Chen <chen...@apache.org>
Subject Re: specificity in selecting EntityMentions when using AggregatePlaintextUMLSProcessor
Date Wed, 04 Sep 2013 02:12:39 GMT
You're right, it should have gotten "CIN I"- that's a strange one,
probably needs to be debugged/looked into further...

On Tue, Sep 3, 2013 at 10:05 PM, Miller, Timothy
<Timothy.Miller@childrens.harvard.edu> wrote:
> Ah. So it will get
> CIN 2 (in SNOMED)
> CIN 3 (in SNOMED)
> but the rest are not in SNOMED?
> I wonder why it doesn't get CIN I? It looks like that exists in SNOMED
> (though I don't fully understand what all the symbols mean in the umls
> browser).
>> CIN I - Cervical intraepithelial neoplasia 1
>> [A3002690/SNOMEDCT/SY/285836003]
> On 09/03/2013 09:55 PM, Pei Chen wrote:
>> 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
>> contain (MeSH, SNOMEDCT, RxNORM, NCI, ICD9) IRRC.
>> --Pei
>> 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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