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From Peter Klügl <peter.klu...@averbis.com>
Subject Re: Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives
Date Fri, 09 Oct 2015 13:58:20 GMT
Hi,

great :-)

The ANNIE Tokenizer and Sentence Splitter will maybe best be replaced by
the coresponding cTAKES components. The ruta word-level features can
then additionally come in handy for token classes.

Best,

Peter

Am 09.10.2015 um 15:42 schrieb Azad Dehghan:
> Peter,
>
> I do have full IP for the files that matter: rule-set, dictionaries, and
> the TwoPass implementation. ANNIE Tokeniser and Sentence splitter won't be
> 'ported' (?) as RUTA provides the required word-level features used by the
> rule-set.
>
> Azad
>
> On 9 October 2015 at 14:32, Peter Klügl <peter.kluegl@averbis.com> wrote:
>
>> Hi,
>>
>> do you have full IP for all files in the sourceforge project? ... e.g.,
>> the files in GATE/plugins/ANNIE/ or GATE/plugins/ANNIE/resources/gazetteer/
>>
>> Best,
>>
>> Peter
>>
>> Am 08.10.2015 um 21:44 schrieb Azad Dehghan:
>>> Hi Pei,
>>>
>>> The licence has now been updated.
>>>
>>> @Andy the licencing is up to the IP holder.
>>>
>>> Cheers,
>>> 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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