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From Pei Chen <chen...@apache.org>
Subject Re: Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives
Date Tue, 03 Nov 2015 15:12:24 GMT
Thanks Peter.

I’ve been swamped lately.

But one item that we need to review is the 3rd party libs jars that
were included to ensure compatibility.  I’ll be sure to take a look at
that over the next few weeks.

—Pei

On Tue, Nov 3, 2015 at 10:10 AM, Peter Klügl <peter.kluegl@averbis.com> wrote:
> Yes, I will do that.
>
> Who else plans to provide patches for it? Just to avoid duplicate work
> and to coordnate the efforts ...
>
> Is there a development dataset which was utilized for the initial
> development, and if yes, is it possible to contribute it too?
>
> My first step would be:
> - set up a maven project
> - set up a development pipeline in a test (with cTAKES components
> replacing the previous ANNIE preprocessing)
>
> Best,
>
> Peter
>
> Am 02.11.2015 um 18:04 schrieb Pei Chen:
>> Hi Peter/Azad,
>> Per INFRA-10579, since there is only a limited history, they suggested
>> we do the export/import ourselves.
>> The initial code base has been imported into:
>> sandbox/ctakes-clinical-deid
>>
>> Feel free to do an svn co
>> https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-clinical-deid/
>> and attach any patches to CTAKES-384 until you have commit access...
>>
>> --Pei
>>
>>
>> On Mon, Nov 2, 2015 at 3:56 AM, Peter Klügl <peter.kluegl@averbis.com> wrote:
>>> Hi,
>>>
>>> I just wanted to ask about the current status. I assume that the source
>>> is not yet in svn, right? Let me know when I can do something (in case I
>>> miss some mail on this list).
>>>
>>> Best,
>>>
>>> Peter
>>>
>>> Am 13.10.2015 um 21:17 schrieb Pei Chen:
>>>> Thanks Azad.
>>>> I submitted a Jira to infra to help us do the import (that way we will try
>>>> and preserve the commit history).
>>>> In the meantime, would you mind filling out the ICLA[1].
>>>>
>>>> [Reminder: Let's keep it in sandbox and not release it until all of the 3rd
>>>> party dependencies licenses have been verified.]
>>>>
>>>> [1] http://www.apache.org/licenses/#clas
>>>>
>>>> Thanks,
>>>> Pei
>>>>
>>>>     Pei Chen
>>>> Wired Informatics <http://www.wiredinformatics.com>
>>>> 265 Franklin St Ste 1702
>>>> Boston, MA 02110
>>>> tel: (617) 433-7544
>>>> Pei.Chen@wiredinformatics.com
>>>>
>>>> On Sun, Oct 11, 2015 at 3:51 PM, Azad Dehghan <azad.dehghan@gmail.com>
>>>> wrote:
>>>>
>>>>> 1: Yes. Sorted.
>>>>> 3: Code attached to the Jira.
>>>>>
>>>>> Azad
>>>>>
>>>>> On 8 October 2015 at 20:03, Chen, Pei <Pei.Chen@childrens.harvard.edu>
>>>>> wrote:
>>>>>
>>>>>> This is great news!
>>>>>>> What is the current status and procedure? Is there an explicit
>>>>>> contribution to cTAKES? Is there an ICLA? What about the license
of the
>>>>>> sourceforge project?
>>>>>> Jira has been opened to track this:
>>>>>> https://issues.apache.org/jira/browse/CTAKES-384
>>>>>>
>>>>>> 1) Azad, would you be willing to switch licenses?  I believe it's
>>>>>> currently GNU3 -> ASL 2.0?
>>>>>> 2) Create a project/module in cTAKES sandbox for this
>>>>>> 3) Export/Import sourceforge and attach the code to the Jira initially.
>>>>>> One of the current cTAKES committers can commit it to the repo (Until
>>>>> folks
>>>>>> can commit directly to the ctakes repo directly going forward.)
>>>>>>
>>>>>> -----Original Message-----
>>>>>> From: Peter Klügl [mailto:peter.kluegl@averbis.com]
>>>>>> Sent: Thursday, October 08, 2015 8:06 AM
>>>>>> To: dev@ctakes.apache.org
>>>>>> Subject: Re: Combining Knowledge- and Data-driven Methods for
>>>>>> De-identification of Clinical Narratives
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I can offer my help here if required.
>>>>>>
>>>>>> I have experience in translating JAPE rules to UIMA Ruta and already
>>>>>> worked with clinical notes, e.g., also concerning deidentification.
>>>>>>
>>>>>> The problem is that I can only invest a few hours in the next two
weeks.
>>>>>> I will have more time next month or even more next year.
>>>>>>
>>>>>> What is the current status and procedure? Is there an explicit
>>>>>> contribution to cTAKES? Is there an ICLA? What about the license
of the
>>>>>> sourceforge project?
>>>>>>
>>>>>> Best,
>>>>>>
>>>>>> Peter
>>>>>>
>>>>>> Am 01.10.2015 um 16:20 schrieb Pei Chen:
>>>>>>> Hi Azad,
>>>>>>> This is awesome news.  Thanks for adding in the code that was
>>>>>>> referenced by the paper.  I'll create a Jira to track we need
to port
>>>>>>> it over to UIMA/Ruta.
>>>>>>>
>>>>>>> In the meantime, the link is at:
>>>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_p_
>>>>>>>
>>>>> clinical-2Ddeid_code_ci_master_tree_&d=BQICaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m=yjhqco4EH0XrR798kbkzfYcFQ8z8MR9UF8mMRSjKTH0&s=_k7AbwzkVrRwTrNC3LArZ5hQ5Q47eh06KCDla7UBugY&e=
>>>>>> for those who may be interested in helping out...
>>>>>>> --Pei
>>>>>>>
>>>>>>> Hello Pei,
>>>>>>>
>>>>>>> I hope all is well.
>>>>>>>
>>>>>>> I have now uploaded the source code for cDeid
>>>>>>> (https://urldefense.proofpoint.com/v2/url?u=http-3A__sourceforge.net_p
>>>>>>> _clinical-2Ddeid_code_ci_master_tree_&d=BQICaQ&c=qS4goWBT7poplM69zy_3x
>>>>>>> hKwEW14JZMSdioCoppxeFU&r=huK2MFkj300qccT8OSuuoYhy_xEYujfPwiAxhPVz5WY&m
>>>>>>>
>>>>> =yjhqco4EH0XrR798kbkzfYcFQ8z8MR9UF8mMRSjKTH0&s=_k7AbwzkVrRwTrNC3LArZ5hQ5Q47eh06KCDla7UBugY&e=
>>>>>> ) ; I have tried to make the code as portable and modular as possible
>>>>> with
>>>>>> some trade-off for performance. This should help with porting the
code to
>>>>>> cTAKES/UIMA.
>>>>>>> Once you let the community know I will try to get involved to
help
>>>>>>> with translating JAPE to RUTA, etc.
>>>>>>>
>>>>>>> Best,
>>>>>>> Azad
>

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