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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 Fri, 06 Nov 2015 15:40:49 GMT
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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