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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 Thu, 28 Jan 2016 13:43:50 GMT
patch applied.
Thanks,
Pei

On Thu, Jan 28, 2016 at 4:14 AM, Peter Klügl <peter.kluegl@averbis.com> wrote:
> Hi Pei,
>
> can you commit the recent patch for us?
>
> CTAKES-384-20160120.patch
>
> Best,
>
> Peter
>
> Am 20.01.2016 um 19:35 schrieb Pei Chen:
>> Hi,
>> Sorry I was swamped recently.
>> But yeah, we can even create an extended type system to store these items temporarily
and add them into the main/core type system afterwards.
>> There was an existing item to upgrade UIMA, but agreed- it will require much more
testing.  If it works, we can upgrade it in our sandbox area or create a branch if necessary.
>>
>> —Pei
>>
>>> On Jan 18, 2016, at 9:06 AM, 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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