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From John Green <john.travis.gr...@gmail.com>
Subject Re: Next cTAKES release (3.1)?
Date Tue, 02 Jul 2013 21:19:28 GMT
Hi all,

Ive been following this mail list for a couple of months. Im a third year medical student
rounding the bend toward my MD. I used to be a computer programmer, however, and continue
my own projects. Im very interested in contributing eventually to cTakes development. In the
meantime, given the current talk of examples, if any domain specific examples needed generated
I am domain knowledgable enough that I could pound out a few free text notes made to order.

Let me know, you all may already have docs on hand willing todo this, but if not...

John Green

Sent from my iPhone

On Jun 28, 2013, at 8:59, "Chen, Pei" <Pei.Chen@childrens.harvard.edu> wrote:

> I completely agree with making cTAKES easier use.  I think it is exciting to hear the
different use cases here and understanding where some of the areas that need improvements
are (which we haven't thought about earlier).
> I think Tim's suggestions and the 3 concrete actionable items makes a lot of sense. 
Hopefully it should attract new users, adopters, and perhaps more committers.
> 
>> i) Make the typesystem forefront in documentation -- generate javadocs and
>> have as a link on the ctakes frontpage/sidebar
>> ii) Similar to the way that we are aiming to have tests in every module, also
>> have clearly labeled examples in every module that set up a pipeline, run on
>> sample notes (could be the same sample notes from the tests), and do
>> something with the results.
>> iii) Follow Giri's recommendation to have example training data for people
>> who want to take the next step and train their own models
> 
> I think Java developers are accustomed to including a library as a dependency/jar, have
an API to pass input, and get the results via pojos;  So the examples could initially shield
the complexity of wiring a pipeline together etc.  
> If we can improve the API's and how it gets integrated with other apps, we can add any
GUI/CLI tools on top of this afterwards.
> 
> --Pei
> 
>> -----Original Message-----
>> From: Miller, Timothy [mailto:Timothy.Miller@childrens.harvard.edu]
>> Sent: Friday, June 28, 2013 8:00 AM
>> To: dev@ctakes.apache.org
>> Subject: Re: Next cTAKES release (3.1)?
>> 
>> Very interesting discussion. I think Giri is right about giving example training
>> data in the format that our training code can read. While our ultimate goal
>> would be to build and release models that are completely domain-
>> independent, in the real world it is almost always better to use some
>> domain-specific data and we should think more about how to facilitate that.
>> 
>> As for making it easier to get started, it is not totally clear to me what this
>> means/how to do it so it might be useful to get specific about what this
>> means. I think our biggest hurdle is
>> 
>> 1) Prerequisite of understanding UIMA/UIMAFit
>> 
>> Since UIMAFit is officially becoming part of UIMA that will be easier, and
>> hopefully people will just learn the easier (in my opinion) UIMAFit way than
>> the standard UIMA way of doing things. Is there something we can be doing
>> to make understanding UIMA easier? Or do we just need to say upfront that
>> this is a prerequisite and hope that people don't give up due to this thing that
>> is out of our control?
>> 
>> Another hurdle is:
>> 
>> 2) cTAKES is a multi-purpose developer-aimed tool
>> 
>> So it's not just a matter of hiding complexity -- at some point people have to
>> understand their problem, understand cTAKES' capabilities, and start coding.
>> Pei's GUI will help for some common use cases but will not remove the
>> requirement that someone at the organization knows cTAKES.
>> I think one part of this problem is the fact that the typesystem is not well
>> documented. A developer needs to know what the output is (objects from
>> the typesystem), how to get them (which modules/pipelines), and what
>> information is in them. So maybe on this end my recommendation would be:
>> i) Make the typesystem forefront in documentation -- generate javadocs and
>> have as a link on the ctakes frontpage/sidebar
>> ii) Similar to the way that we are aiming to have tests in every module, also
>> have clearly labeled examples in every module that set up a pipeline, run on
>> sample notes (could be the same sample notes from the tests), and do
>> something with the results.
>> iii) Follow Giri's recommendation to have example training data for people
>> who want to take the next step and train their own models
>> 
>> This is quite a bit of developer overhead, so it's worth asking whether you
>> agree with my "diagnosis" and "treatment" or whether you think there are
>> different problems/solutions that should be higher priority.
>> 
>> Tim
>> 
>> On 06/27/2013 10:59 PM, Girivaraprasad Nambari wrote:
>>> Hi Vijay and Andy,
>>> 
>>> Thanks for sharing those examples.
>>> 
>>> "Trouble is, privacy requires that these examples be made up by hand"
>>> 
>>> Agree with this statement and this is very valid concern.
>>> 
>>> In "getting started examples", I think we should just have couple of
>>> entries (5-10 small entries), not more than that (with explicit
>>> statement like "ONLY EXAMPLE", NOT GOOD FOR REAL USAGE). I
>> understand
>>> handcrafting these may not be easy because we are not medical domain
>>> experts, but I feel worth time, because it brings in more user community.
>>> 
>>> Thank you,
>>> Giri
>>> 
>>> 
>>> 
>>> 
>>> 
>>> On Thu, Jun 27, 2013 at 10:25 PM, Andy McMurry
>> <mcmurry.andy@gmail.com>wrote:
>>> 
>>>> GREAT !
>>>> 
>>>> The i2b2 data though isn't publicly distributable, you still need to
>>>> request access to it since it is "semi private"
>>>> 
>>>> 
>>>> On Jun 27, 2013, at 9:52 PM, vijay garla <vngarla@gmail.com> wrote:
>>>> 
>>>>> We released code on using cTAKES to annotate clinical text and SVMs
>>>>> that use the annotations to classify clinical text from the CMC 2007
>>>>> and I2B2
>>>>> 2008 challenges:
>>>>> 
>>>>> We did the cmd 2007 with cTAKES 2.5:
>> https://code.google.com/p/ytex/wiki/WordSenseDisambiguation_V08#Repr
>> o
>>>> ducing_results_on_CMC_2007_challenge
>>>> <https://code.google.com/p/ytex/downloads/list>
>>>>> 
>>>>> And the i2b2 2008 with the version of cTAKES distributed with the
>>>>> first version of ARC:
>>>>> https://code.google.com/p/ytex/wiki/FeatEng_V05#i2b2_2008
>>>>> 
>>>>> These are both publicly available datasets, and represent real-world
>>>>> problems (in general I believe when publishing a paper the code
>>>>> should be reproducible and made publicly available, but that's a different
>> issue).
>>>>> 
>>>>> When we get around to upgrading YTEX to cTAKES 3.1, we would like to
>>>>> upgrade these samples as well.
>>>>> 
>>>>> Best,
>>>>> 
>>>>> VJ
>>>>> 
>>>>> 
>>>>> 
>>>>> On Thu, Jun 27, 2013 at 8:32 PM, Andy McMurry
>>>>> <mcmurry.andy@gmail.com
>>>>> wrote:
>>>>> 
>>>>>> +1 suggestion for documenting many examples of "getting started"
>>>>>> +NLP
>>>>>> datasets.
>>>>>> 
>>>>>> I have at least one we can use that was created by our lead
>>>>>> Pathologist
>> https://open.med.harvard.edu/svn/scrubber/releases/3.0/data/input/cas
>>>> es/train/traincase.xml
>>>>>> We should provide at least one sample for each domain.
>>>>>> Trouble is, privacy requires that these examples be made up by hand
>>>>>> and not copy-pasted from EMR systems.
>>>>>> 
>>>>>> --Andy
>>>>>> 
>>>>>> On Jun 27, 2013, at 5:32 PM, Girivaraprasad Nambari <
>>>> girinambari@gmail.com>
>>>>>> wrote:
>>>>>> 
>>>>>>> +1 for this observation Andy!
>>>>>>> 
>>>>>>> Lowering time will motive users in writing blogs about features,
>>>>>>> how
>>>> to,
>>>>>>> etc., which reduces core team work load on documentation.
>>>>>>> 
>>>>>>> I have been trying to write a small "how to write standalone
>>>>>>> client for ctakes" with my experience (I saw at least 4 users
>>>>>>> posted similar
>>>>>> question
>>>>>>> in last 2 months), but not getting enough time because ctakes
>>>>>>> depends
>>>> on
>>>>>>> lot of other frameworks (UimaFit, cleartk, UIMA Framework etc.,),
>>>>>>> most
>>>> of
>>>>>>> my spare time is being spent on juggling between these frameworks,
>>>>>> posting
>>>>>>> and browsing those forums, relating observations to ctakes code.
I
>>>> think
>>>>>> we
>>>>>>> need to have some high level documentation about these (with
links
>>>>>>> to corresponding forums).
>>>>>>> 
>>>>>>> Above case is for developers (I think this will be more user
base
>>>>>>> as
>>>>>> ctakes
>>>>>>> progress), for users I think documentation is lot better though
>>>>>>> some improvements need to be done.
>>>>>>> 
>>>>>>> As a developer I felt tough with lack of sample training data
(I
>>>>>>> am
>>>> still
>>>>>>> struggling in this area even though I browsed all relevant code),
>>>> though
>>>>>>> training class are there. I understood that there are licensing
>>>>>>> issues
>>>>>> with
>>>>>>> REAL data, but at least some hand made example sentences, which
>>>>>>> may not
>>>>>> be
>>>>>>> real but helps developers in understanding the type/structure
of
>>>>>>> input TRAINING classes expecting. This way people who browse
the
>>>>>>> code can
>>>>>> reverse
>>>>>>> engineer and develop their own models. Sorry if you guys feel
this
>>>>>>> as novice issue, but I feel most of the developers will be novice
>>>>>>> when
>>>> they
>>>>>>> adopt a system and Machine Learning/NLP is ocean. Some
>>>>>>> documentation in this area will same lot of time for us.
>>>>>>> 
>>>>>>> I wish there will be some activity in this area from ctakes core
team.
>>>>>>> 
>>>>>>> Thank you,
>>>>>>> Giri
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> On Thu, Jun 27, 2013 at 5:11 PM, Andy McMurry
>>>>>>> <mcmurry.andy@gmail.com
>>>>>>> wrote:
>>>>>>> 
>>>>>>>> ctakes is at a point where we have a LOT of features but
it is
>>>>>>>> still
>>>>>> hard
>>>>>>>> to get started.
>>>>>>>> 
>>>>>>>> Judging from the mailing lists a lot of how cTakes works
is not
>>>> obvious
>>>>>>>> and requires hand holding.
>>>>>>>> This is very typical in early FOSS projects.
>>>>>>>> 
>>>>>>>> Lowering the time to get invested in ctakes gets more users
AND
>>>>>>>> better
>>>>>> bug
>>>>>>>> reports, FAQ, etc.
>>>>>>>> 
>>>>>>>> thoughts?
>>>>>>>> --Andy
>>>>>>>> 
>>>>>>>> 
>>>>>>>> On Apr 11, 2013, at 8:55 PM, "Chen, Pei" <
>>>>>> Pei.Chen@childrens.harvard.edu>
>>>>>>>> wrote:
>>>>>>>> 
>>>>>>>>> Hi,
>>>>>>>>> I just wanted to gauge the interest of creating the next
release
>>>>>>>>> of
>>>>>>>> cTAKES (3.1) which is currently marked for May in Jira-
>>>>>>>>> There have already been 22/53 issues [1] marked as fixed
or closed.
>>>>>>>> Plenty of bug fixes and new components including:
>>>>>>>>> - New CEM Instance Template population
>>>>>>>>> - New Dependency Parser/Semantic Role Labeler
>>>>>>>>> - New optional Clear POSTagger
>>>>>>>>> - New regression testing component
>>>>>>>>> 
>>>>>>>>> Should we wait for the Temporal component?
>>>>>>>>> 
>>>>>>>>> [1]
>> https://issues.apache.org/jira/issues/?jql=fixVersion%20%3D%20%223.1%
>>>> 22%20AND%20project%20%3D%20CTAKES
> 

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