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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 Mon, 02 Nov 2015 17:04:34 GMT
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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