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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 Tue, 24 Nov 2015 09:57:01 GMT

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.



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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