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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 Wed, 20 Jan 2016 00:47:47 GMT
Peter,

So, we have Email, Url, Profession, Street, Zip, State and Username
completed so far.

The following NERs remain:
Country, Age, Doctor, Fax, Id_num, Medicalrec_num, Patient, and Phone.

I will do Country next. If you are able to translated the rest quickly
please do :) else just keep me posted which ones your are working on to
avoid duplicate work...and we can work through the remaining NERs.

Also, once the NERs are translated I will prepare a number of examples for
unit testing -- I will also be validate the NERs using the i2b2 research
dataset.

Cheers,
Azad

On 19 January 2016 at 09:01, Peter Klügl <peter.kluegl@averbis.com> wrote:

> Ok, let me know which ones I should translate.
>
> Best,
>
> Peter
>
> Am 18.01.2016 um 20:13 schrieb Azad Dehghan:
> > Peter,
> >
> > Thanks for pushing things!
> >
> > I would rather split the rules/NERs to get things moving quicker (as I
> am a
> > newbie to Ruta). I will be uploading another NER (Username) shortly. I
> will
> > look at your changes to follow suit.
> >
> > Best,
> > Azad
> >
> > On 18 January 2016 at 14:06, Peter Klügl <peter.kluegl@averbis.com>
> wrote:
> >
> >> Hi,
> >>
> >> a new patch is attached.
> >>
> >> @Pei:
> >> are there suitable annotation types in the cTAKES type system? Some
> >> project in cTAKES uses something like OntologyMatch... I map it to
> >> IdentifiedAnnotation right now, but there are many empty features...
> >>
> >> @Azad:
> >> I changed the rules a bit, especially the capitalization like I use it
> >> in ruta normally. The wordlist are compiled to a trie by the maven
> >> plugin. I also added the two regexes for url and email. I extended the
> >> regex for the url. I also changed the evaluation order of some rules
> >> (with @). Feel free to add simple examples to examples.csv for the unit
> >> tests.
> >>
> >> Let me know if you need more information about the changes.
> >>
> >> Do you wanna have help with the other rule sets? Or should we split them
> >> up?
> >>
> >> Best,
> >>
> >> Peter
> >>
> >> Am 18.01.2016 um 11:04 schrieb Peter Klügl:
> >>> Hi,
> >>>
> >>> great. I will integrate them in the project and in the next patch.
> >>>
> >>> Best,
> >>>
> >>> Peter
> >>>
> >>> Am 18.01.2016 um 00:58 schrieb Azad Dehghan:
> >>>> 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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