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From "Finan, Sean" <Sean.Fi...@childrens.harvard.edu>
Subject RE: specificity in selecting EntityMentions when using AggregatePlaintextUMLSProcessor
Date Wed, 04 Sep 2013 13:49:42 GMT
This may sound strange, but SNOMED does not contain the term "CIN I".  It contains the terms
"CIN I - Cervical intraepitheal neoplasia 1" and "CIN I - mild dyskaryosis".  

-----Original Message-----
From: Pei Chen [mailto:chenpei@apache.org] 
Sent: Tuesday, September 03, 2013 10:13 PM
To: dev@ctakes.apache.org
Subject: Re: specificity in selecting EntityMentions when using AggregatePlaintextUMLSProcessor

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 III (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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>

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