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From: "Savova, Guergana" <Guergana.Savova@childrens.harvard.edu>
To: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
CC: Rohit Shinde <rohit.shinde12194@gmail.com>
Subject: RE: Medical de-identification
Thread-Topic: Medical de-identification
Thread-Index: AQHQZLkpABA5Jy3T8kic7YvW7Zzn8Z0orEOg
Date: Sun, 22 Mar 2015 16:12:04 +0000
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Agreed - sounds very good!
--guergana

From: britt fitch [mailto:britt.fitch@wiredinformatics.com]
Sent: Sunday, March 22, 2015 11:59 AM
To: dev@ctakes.apache.org
Cc: Rohit Shinde
Subject: Re: Medical de-identification

Sounds good.

Starting with some references:
Docs: https://open.med.harvard.edu/wiki/display/SCRUBBER/3.X
Publication: http://www.biomedcentral.com/1472-6947/13/112/abstract<https:/=
/urldefense.proofpoint.com/v2/url?u=3Dhttp-3A__www.biomedcentral.com_1472-2=
D6947_13_112_abstract&d=3DBQMFAg&c=3DqS4goWBT7poplM69zy_3xhKwEW14JZMSdioCop=
pxeFU&r=3DSeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP&=
m=3DbElqtqimbSGc3Cbyxp1_oNRMbbZ9w7mScUEcNhes2TM&s=3Djgyc3gCZWJdxamCiymz-V4a=
zLkLAs3bma06lfliuU34&e=3D>  (check out the supplemental material as well fo=
r additional details on running and improvements)
SVN (old, standalone, Scrubber v.3.x): https://open.med.harvard.edu/wiki/di=
splay/SCRUBBER/Software
SVN (initial apache port to ctakes sandbox): https://svn.apache.org/repos/a=
sf/ctakes/sandbox/ctakes-scrubber-deid/<https://urldefense.proofpoint.com/v=
2/url?u=3Dhttps-3A__svn.apache.org_repos_asf_ctakes_sandbox_ctakes-2Dscrubb=
er-2Ddeid_&d=3DBQMFAg&c=3DqS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=3DS=
eLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr-rCmP&m=3DbElqtqi=
mbSGc3Cbyxp1_oNRMbbZ9w7mScUEcNhes2TM&s=3DciZ3kN8xH-3Rqmi1RE_YryRHMpohi7t-XV=
1w3prNiN4&e=3D>

The project started off as a standalone process and became a UIMA pipeline =
(outside of ctakes).
The plan had always been to port this to an optional ctakes module but we n=
ever got that fully implemented.

Some of the parts that need the most attention to get going:

  *   working with the ctakes type system
  *   pulling out weka (ML lib) for an asf 2.0 friendly lib instead
  *   simpler process for building the models.

Regarding knowledge, its good to be familiar with java, UIMA, decision tree=
s, and ctakes. Likely in that order.

While this is still in the sandbox and you are still getting familiar with =
running it as a standalone app feel free to ping me and andy off-list if th=
ats more convenient.
Then we can definitely bring it back to the dev list while getting it runni=
ng in ctakes.

Cheers,

Britt


Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com<https://urldefense.proofpoint.com/v2/url?u=3Dht=
tp-3A__wiredinformatics.com&d=3DBQMFAg&c=3DqS4goWBT7poplM69zy_3xhKwEW14JZMS=
dioCoppxeFU&r=3DSeLHlpmrGNnJ9mI2WCgf_wwQk9zL4aIrVmfBoSi-j0kfEcrO4yRGmRCJNAr=
-rCmP&m=3DbElqtqimbSGc3Cbyxp1_oNRMbbZ9w7mScUEcNhes2TM&s=3DolOk8tiCOBwBEe2T2=
e5QjL3HkZhJMbV22Xdx-QqdYjA&e=3D>
Britt.Fitch@wiredinformatics.com<mailto:Britt.Fitch@wiredinformatics.com>

On Mar 20, 2015, at 7:57 PM, andy mcmurry <mcmurry.andy@gmail.com<mailto:mc=
murry.andy@gmail.com>> wrote:

Britt et al: here is a student named rohit interested in getting the
deidentification pipeline running again. Hoping there is still interest in
getting this going in ctakes for real. Comments?
---------- Forwarded message ----------
From: "Rohit Shinde" <rohit.shinde12194@gmail.com<mailto:rohit.shinde12194@=
gmail.com>>
Date: Mar 20, 2015 5:02 AM
Subject: Re: Medical de-identification
To: "andy mcmurry" <mcmurry.andy@gmail.com<mailto:mcmurry.andy@gmail.com>>
Cc:

I would certainly be interested into "production grade code". The project
also sounds interesting. How do I start working on it? I know Java well.
What else would I need to know before starting on this project?

On Fri, Mar 20, 2015 at 12:44 PM, andy mcmurry <mcmurry.andy@gmail.com<mail=
to:mcmurry.andy@gmail.com>>
wrote:


Yes, the project is in Java, the code was written for a research project
and never made into "production grade code". If you are interested, we
would like to turn the scrubber into a solid pipeline. Java programming
100%, with Colt statistical library
On Mar 19, 2015 7:52 PM, "Rohit Shinde" <rohit.shinde12194@gmail.com<mailto=
:rohit.shinde12194@gmail.com>>
wrote:


Hi Andy,

Could you please tell me more about that project? I would really like a
reply.

Thank you,
Rohit Shinde

On Wed, Mar 18, 2015 at 5:51 PM, Rohit Shinde <
rohit.shinde12194@gmail.com<mailto:rohit.shinde12194@gmail.com>> wrote:


Hi Andy,

I am interested in medical de-identification. I would like to know what
this project consists of. Is it partially implemented, or does the
implementation need to start?

What languages would I need to know? What theoretical background would I
need? Also, how complex would this task be? What parts of OpenNLP does this
project use?

Thank you,
Rohit Shinde


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