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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, 19 Jan 2016 09:01:26 GMT
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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