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From britt fitch <britt.fi...@wiredinformatics.com>
Subject Re: Medical de-identification
Date Sun, 22 Mar 2015 15:58:32 GMT
Sounds good.

Starting with some references:
Docs: https://open.med.harvard.edu/wiki/display/SCRUBBER/3.X <https://open.med.harvard.edu/wiki/display/SCRUBBER/3.X>
Publication: http://www.biomedcentral.com/1472-6947/13/112/abstract <http://www.biomedcentral.com/1472-6947/13/112/abstract>
 (check out the supplemental material as well for additional details on running and improvements)
SVN (old, standalone, Scrubber v.3.x): https://open.med.harvard.edu/wiki/display/SCRUBBER/Software
<https://open.med.harvard.edu/wiki/display/SCRUBBER/Software>
SVN (initial apache port to ctakes sandbox): https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-scrubber-deid/
<https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-scrubber-deid/>

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 never 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 trees, 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 thats more convenient.
Then we can definitely bring it back to the dev list while getting it running in ctakes.

Cheers,

Britt


Britt Fitch
Wired Informatics
265 Franklin St Ste 1702
Boston, MA 02110
http://wiredinformatics.com
Britt.Fitch@wiredinformatics.com

> On Mar 20, 2015, at 7:57 PM, andy mcmurry <mcmurry.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>
> Date: Mar 20, 2015 5:02 AM
> Subject: Re: Medical de-identification
> To: "andy mcmurry" <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>
> 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>
>> 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> 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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