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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 Fri, 29 Jan 2016 09:34:34 GMT

the problems were caused by the svn client in my Eclipse. Sorry for the
trouble, I should have looked more closely at the ciomplete patch.

I attached a new patch created with commandline tools wich looks correct

Pei, can you apply the new patch?



Am 28.01.2016 um 15:57 schrieb Peter Klügl:
> Thanks Pei.
> I fear there was again a problem with the patch. All new files are
> missing (and also the svn-ignore settings).
> Can you take a look?
> Best,
> Peter
> Am 28.01.2016 um 14:43 schrieb Pei Chen:
>> 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>
>>>>> 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
>>>>> 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 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
>>>>>>>>>>> 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
>>>>>>>> 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
>>>>>>>>>>> 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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