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Date: Tue, 30 Sep 2014 11:43:35 -0700 (PDT)
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From: "John Green" <john.travis.green@gmail.com>
To: dev@ctakes.apache.org
Cc: dev@ctakes.apache.org
Subject: Re: De-identified lab tests dataset
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I could pull a dozen or so =22sets=22 of labs from my own personal bank of =
notes that contain various forms of what you would usually call the lab =
section of a soap note with minimal effort .... I dont mind, might take me =
a couple of days with work tempo as it is. Its probably all from of two =
different emr's total though with a handfull of written values in short =
hand=C2=A0(E.g the classic fishbones used for like bnp and cbc), so not a =
lot of variability but maybe enough to start compiling regex's with.


If thats helpful and no one else comes along with some free data of a =
larger sort...


Also, there are about 10 notes I commited to the project a year or so ago =
as examples that may have lab data in them.


JG
=E2=80=94
Sent from Mailbox

On Tue, Sep 30, 2014 at 8:25 AM, Ajay Jain <ajayjain@mobileinsights.net>
wrote:

> John,
> I am in the initial stages of my project and I'll take whatever dataset =
you are able to provide without spending a lot of effort extracting it.=20
> Thanks.
> Ajay
> Sent from my iPhone
>> On Sep 30, 2014, at 5:22 AM, =22John Green=22 <john.travis.green@gmail.=
com> wrote:
>>=20
>> How large=3F And across how many EMRs=3F=20
>>=20
>>=20
>> JG
>> =E2=80=94
>> Sent from Mailbox
>>=20
>> On Mon, Sep 29, 2014 at 6:58 PM, Ajay Jain <ajayjain@mobileinsights.=
net>
>> wrote:
>>=20
>>> Sorry, I wasn't clear. I am working on a related project and trying to =
figure out if the code can be repurposed for a lab mention annotator for =
cTAKES. From what I have seen, test names from different institutions are =
not standardized which makes it hard to standardize the resulting =
annotation. Getting access to a larger lab tests dataset (structured) will =
help me fine tune the model.=20
>>>=20
>>> Hope this helps.=20
>>> Ajay
>>> Sent from my iPhone
>>>> On Sep 29, 2014, at 2:12 PM, =22Savova, Guergana=22 <Guergana.=
Savova@childrens.harvard.edu> wrote:
>>>>=20
>>>> Ajay,
>>>> cTAKES currently does not implement a method to discover labs from the=
 text. The motivation is that you can get that easily from the structured =
part of the EMR (what Pete explained below). Hope this makes sense!
>>>> --Guergana
>>>>=20
>>>> -----Original Message-----
>>>> From: Peter Szolovits [mailto:psz@mit.edu]=20
>>>> Sent: Monday, September 29, 2014 2:32 PM
>>>> To: dev@ctakes.apache.org
>>>> Subject: Re: De-identified lab tests dataset
>>>>=20
>>>> Ajay, I'm confused by your query.  cTakes is good at interpreting text=
, but most lab test results are reported in tabular form that is most =
appropriately searched by SQL queries.  Sometimes lab results are also =
reported in narrative notes, but parsing those is often more a matter of =
deciphering the text structure of tables than of parsing real English text.=
  What am I misunderstanding=3F
>>>>=20
>>>> --Pete Sz.
>>>>=20
>>>>> On Sep 29, 2014, at 2:25 PM, Ajay Jain <ajayjain@mobileinsights.net> =
wrote:
>>>>>=20
>>>>> Hello All,
>>>>>=20
>>>>> I am working on a use case for lab tests data using cTAKES and my=20
>>>>> online search to find a test dataset has been futile.  I'll =
greatly=20
>>>>> appreciate if someone can share such a dataset or can point me in =
the=20
>>>>> right direction to go looking for one.
>>>>>=20
>>>>> Best,
>>>>> Ajay
>>>>>=20
>>>>> --
>>>>> Founder & CEO
>>>>> Mobile Insights, Inc.
>>>>> (630) 408-8623
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