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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 Thu, 28 Jan 2016 09:14:23 GMT
Hi Pei,

can you commit the recent patch for us?




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>
>>>>> 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>
>>>>>> 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
>>>>>>> generate desc's as secondary...
>>>>>>> I think the actual components that would be required is probably
>>>>>>> left up to what is actually required for best performing c-deid.
>>>>>>> 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
>>>>>>> alternative JCas view.  You can probably open up that discussion
>>>>>>> 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
>>>>> different
>>>>>>>> manner and I do not what to get inspired by "some sort of
>>>>>>>> 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:
>>>>> ...
>>>>>>>> parser, ... dict lookup?
>>>>>>>> "output": Should the project provide a pipeline or a single
>>>>>>>> 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;
>>>>>>>>> <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
>>>>>>>> Ok, I'll investigate if we have already access to the dataset
>>>>>>>>>> My first step would be:
>>>>>>>>>> - set up a maven project
>>>>>>>>>> - set up a development pipeline in a test (with cTAKES
>>>>>>>>>> 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
>>>>> for
>>>>>>>>> the Two Pass recognition (TwoPass.java) as this method
have shown
>>>>> useful
>>>>>>>>> for general NER on longitudinal data and surely useful
>>>>> of the
>>>>>>>>> deid component.
>>>>>>>>> Cheers,
>>>>>>>>> Azad

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