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From Azad Dehghan <azad.dehg...@gmail.com>
Subject Re: Combining Knowledge- and Data-driven Methods for De-identification of Clinical Narratives
Date Sun, 17 Jan 2016 23:58:44 GMT
Three NERs translated and uploaded.

PS. I will validate all NERs once we have them all completed.

Cheers,
Azad

On 24 November 2015 at 10:37, Azad Dehghan <azad.dehghan@gmail.com> wrote:

> 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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