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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 14:57:36 GMT
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>
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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