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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, 06 Nov 2015 08:38:26 GMT
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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