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From Pei Chen <pei.c...@wiredinformatics.com>
Subject Re: Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives
Date Mon, 11 Jan 2016 22:52:19 GMT
Patch applied:
http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-clinical-deid/ <http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-clinical-deid/>
Thanks Peter.

What error did you get with xml-api’s?  Do you mean upgrade ctakes to the latest version
of uima instead of 2.4.0?

—Pei

> On Jan 11, 2016, at 12:39 PM, Peter Klügl <peter.kluegl@averbis.com> wrote:
> 
> Hi,
> 
> I just added a small patch which adds a maven build process and a dummy
> unit test.
> 
> I had some problems with the version of xml-apis. Is this known or
> rather a local problem on my build machine?
> Is there a reason why cTAKES requires uima 2.4.0?
> 
> Next step would be translating the rules. Azad mentioned that he already
> started with that :-)
> 
> Best,
> 
> Peter
> 
> 
> Am 18.12.2015 um 11:01 schrieb Peter Klügl:
>> Hi,
>> 
>> sorry, there was no free time left in December for this issue, but I
>> will be able to provide the patches in January (for real).
>> 
>> Best,
>> 
>> Peter
>> 
>> Am 24.11.2015 um 11:37 schrieb Azad Dehghan:
>>> This is on my todo list for Dec. as well. If there are any more volunteers
>>> for translating JAPE to RUTA, please get in touch.
>>> 
>>> Cheers,
>>> Azad
>>> 
>>> On 24 Nov 2015 09:55, "Peter Klügl" <peter.kluegl@averbis.com> wrote:
>>>> Hi,
>>>> 
>>>> I just wanted to mention that I haven't forgot about it. Unfortunately,
>>>> there is just no spare time right now. I hope I will be able to provide
>>>> the patches in December.
>>>> 
>>>> Best,
>>>> 
>>>> Peter
>>>> 
>>>> Am 06.11.2015 um 16:40 schrieb Pei Chen:
>>>>> Hi Peter,
>>>>> I think the ctakes-examples is probably a good starting point at least
>>>>> in terms of maven modules, etc.  I think it would be good if we use
>>>>> uimaFIT style as primary approach to wiring components together and
>>>>> generate desc's as secondary...
>>>>> I think the actual components that would be required is probably best
>>>>> left up to what is actually required for best performing c-deid.  The
>>>>> output would be interesting, I'm not sure if we should treat this as
>>>>> an independent preprocessing component or part of a pipeline (in which
>>>>> case, we may need to propose a change to the type system or perhaps an
>>>>> alternative JCas view.  You can probably open up that discussion to
>>>>> the dev group as you see fit.)
>>>>> 
>>>>> My 2 cents...
>>>>> 
>>>>> 
>>>>> On Fri, Nov 6, 2015 at 3:38 AM, Peter Klügl <peter.kluegl@averbis.com>
>>> wrote:
>>>>>> Hi,
>>>>>> 
>>>>>> Is there a cTAKES project that may serve as an example on how the
>>> cTAKES
>>>>>> community develops or how a project should look like?
>>>>>> I learned that different people set up UIMA project in a quite
>>> different
>>>>>> manner and I do not what to get inspired by "some sort of out-dated"
>>>>>> approach in the cTAKES repo.
>>>>>> 
>>>>>> Are there restriction or preferences about the preprocessing components
>>>>>> that should be used and the kind of "output" of the project.
>>>>>> Components: On which components may the componetns rely: tokenizer,
...
>>>>>> parser, ... dict lookup?
>>>>>> "output": Should the project provide a pipeline or a single AE?
>>>>>> 
>>>>>> More comments below.
>>>>>> 
>>>>>> Am 03.11.2015 um 16:54 schrieb Azad Dehghan:
>>>>>>>> Who else plans to provide patches for it? Just to avoid duplicate
>>> work
>>>>>>>> and to coordnate the efforts ...
>>>>>>>> 
>>>>>>> I would like to help with the translating JAPE to RUTA.
>>>>>> You can already go ahead with the UIMA Ruta Workbench if you want,
or
>>>>>> wait until I set up the project with ruta integration.
>>>>>> 
>>>>>> If any questions arise, just ask :-)
>>>>>> 
>>>>>>>> Is there a development dataset which was utilized for the
initial
>>>>>>>> development, and if yes, is it possible to contribute it
too?
>>>>>>>> 
>>>>>>> The data set is unfortunately not publicly available; i2b2
>>>>>>> <https://www.i2b2.org/NLP/DataSets/Main.php> typically
releases the
>>> data
>>>>>>> sets 12 months after a given challenge; this is done on an individual
>>> basis
>>>>>>> and involve a Data Use Agreement.
>>>>>>> 
>>>>>>> However, I will be able to conduct and coordinate the validation.
>>>>>>> 
>>>>>> Ok, I'll investigate if we have already access to the dataset here.
>>>>>> 
>>>>>> 
>>>>>>>> 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)
>>>>>>>> 
>>>>>>>> 
>>>>>>>> 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
>>>>>>>> 
>>>>>>>> 
>>>>>>> @Pei - once ANNIE components are replaced there is should not
be a
>>> need to
>>>>>>> worry about the 3rd party libs.
>>>>>>> 
>>>>>>> Also, just a thought: we may want to create an independent component
>>> for
>>>>>>> the Two Pass recognition (TwoPass.java) as this method have shown
>>> useful
>>>>>>> for general NER on longitudinal data and surely useful independent
of
>>> the
>>>>>>> deid component.
>>>>>>> 
>>>>>>> 
>>>>>>> Cheers,
>>>>>>> Azad
>>>>>>> 
> 


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