Ted [theodore.as...@providence.org]
Sent: Friday, November 01, 2013 5:36 PM
To: dev@ctakes.apache.org
Subject: RE: specificity in selecting EntityMentions when using
AggregatePlaintextUMLSProcessor
OK, Kind of resurfacing the original topic on this one, after I redirected it
towards ICD codes last month:
AM
To: dev@ctakes.apache.org
Subject: RE: specificity in selecting EntityMentions when using
AggregatePlaintextUMLSProcessor
I don't know if this is exactly what you want, but you can use the hyperSql (
http://hsqldb.org/ ) database tool to perform searches on the umls dictionary
used by cTakes.
For in
User
FAQ's?)
--Pei
> -Original Message-
> From: Vogel, James [mailto:jvo...@activehealth.net]
> Sent: Monday, September 30, 2013 11:41 AM
> To: dev@ctakes.apache.org
> Subject: RE: specificity in selecting EntityMentions when using
> AggregatePlaintextUMLSProcesso
et of ICD9 is in the dictionary?
From: Pei Chen [mailto:chen...@apache.org]
Sent: Friday, September 27, 2013 11:26 PM
To: dev@ctakes.apache.org
Subject: Re: specificity in selecting EntityMentions when using
AggregatePlaintextUMLSProcessor
James,
Obviously it would be best to customize the code and/or the
concepts or do I change the code in consumeHits() or
>> getSnomedCodes()?
>>
>> -----Original Message-
>> From: Vogel, James
>> Sent: Friday, September 27, 2013 6:30 PM
>> To: dev@ctakes.apache.org
>> Subject: RE: specificity in selecting EntityMentions
bles
> in the hsql database that would contain the ICD9 data?
>
> Thanks.
>
> -Original Message-
> From: Miller, Timothy [mailto:timothy.mil...@childrens.harvard.edu]
> Sent: Monday, September 16, 2013 7:25 AM
> To: dev@ctakes.apache.org
> Subject: Re: specificity in selectin
nt: Friday, September 27, 2013 6:30 PM
To: dev@ctakes.apache.org
Subject: RE: specificity in selecting EntityMentions when using
AggregatePlaintextUMLSProcessor
Is anyone able to provide any more detailed guidance on what I'd need to change
to add the ICD9 codes as tags, e.g., where do I look fo
y.mil...@childrens.harvard.edu]
Sent: Monday, September 16, 2013 7:25 AM
To: dev@ctakes.apache.org
Subject: Re: specificity in selecting EntityMentions when using
AggregatePlaintextUMLSProcessor
James,
I haven't done it myself, so I don't know exactly how the config
changes, but I know roughly where t
nd impl that would need to be made to get the ICD9 codes?
>
> -Original Message-
> From: Pei Chen [mailto:chen...@apache.org]
> Sent: Wednesday, September 04, 2013 1:02 PM
> To: dev@ctakes.apache.org
> Subject: Re: specificity in selecting EntityMentions when using
> A
ate the ICD9 for a specific entity?
>
> Thank you
>
> Ted
>
> -Original Message-
> From: Pei Chen [mailto:chen...@apache.org]
> Sent: Tuesday, September 03, 2013 7:13 PM
> To: dev@ctakes.apache.org
> Subject: Re: specificity in selecting EntityMentions when
sanz.James=mayo@ctakes.apache.org] on behalf of Assur,
Ted [theodore.as...@providence.org]
Sent: Wednesday, September 04, 2013 10:55 AM
To: dev@ctakes.apache.org
Subject: RE: specificity in selecting EntityMentions when using
AggregatePlaintextUMLSProcessor
Thanks for looking into this, it'
>
> -Original Message-
> From: Pei Chen [mailto:chen...@apache.org]
> Sent: Tuesday, September 03, 2013 7:13 PM
> To: dev@ctakes.apache.org
> Subject: Re: specificity in selecting EntityMentions when using
> AggregatePlaintextUMLSProcessor
>
> You're right, it
can
find it online ... but that won't do you much good wrt cTakes.
Sean
-Original Message-
From: Assur, Ted [mailto:theodore.as...@providence.org]
Sent: Wednesday, September 04, 2013 11:56 AM
To: dev@ctakes.apache.org
Subject: RE: specificity in selecting EntityMentions when using
Ag
-Original Message-
From: Pei Chen [mailto:chen...@apache.org]
Sent: Tuesday, September 03, 2013 7:13 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&#x
mber 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
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
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?
>
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 ne
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 [A965/SNOMEDCT/SY/20365006] also exists that's why it was
able to perform the look
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 chunk
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 grad
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