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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 Mon, 11 Jan 2016 17:39:52 GMT

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 :-)



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
>>>>> 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
>> 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
>>>>>>> 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
>> 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
>> the
>>>>>> deid component.
>>>>>> Cheers,
>>>>>> Azad

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