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From Hephaestus Studio <hephaestus.stu...@gmail.com>
Subject Re: Next cTAKES release (3.1)?
Date Wed, 03 Jul 2013 21:45:45 GMT
@Andy - Not a doctor yet, but soon! Thanks for the promotion though, one more year! 

- Apropos meds or clinical type questions: any developer on here can feel free to shoot me
a quick question via the list anytime, Id be happy to confirm that a drug or anything else
makes since given a particular clinical/note context. 

- "I wonder if there is someway in which you could guide us in making better use of the medical
knowledge sources (ontologies) that are available." - I'd be happy to brainstorm about using
existing resources to help in decision making. We use these all the time in the clinic.

@ Tim+Andy+Chen - I haven't had a chance to really start chewing into the code, though I hope
to over the next year; so, what kind of examples would be most helpful?
    - Any particular disease processes? 
    - Are you all familiar with the ubiquitous SOAP style presentation that doctors use to
write free notes? The few examples I clicked through in the repository that Chen pointed me
too are very sparse. Would we want gradations? E.g., a scale for "well done" notes to "very
quick I-dont-care-because-I'm-in-a-rush" notes?

@ Chen - Thank you for the kind words. It's nice to be welcomed by a community in which you
hope to integrate. And thank you for pointing me to the directory with the current sample
notes. This was very helpful in determining where those are at in there development. I know
that each of your hospitals have a wealth of HIPAA-closed notes, but I'll see what I can do
to make some "stereotypical" open-notes for common disease presentations. Again: maybe a scale,
not necessarily just on brevity but some other metric, whose continuum represented various
permutations of degrees of something, maybe of difficulty in processing? Apropos code, Chen:
I will help where I can but where I want to be is elbow deep in the code :)

Finally: I haven't had a chance to look into some of the links from earlier in this thread
regarding open access repositories of free text clinical notes: what do you all feel the quality
of these resources are? Abundant but low quality? Paucity but those that are there are high

Bottom line: no problem either answering contextual questions (can afib be associated with
a lower gi bleed??) and no problem writing some notes, only question would be, before I put
in any time: what disease/specialty domain? and would we want some system that put them on
a continuum of some variable, say, brevity or "readability"?

Just thinking before leaping,


Sent from my iPhone

On Jul 2, 2013, at 21:23, "Chen, Pei" <Pei.Chen@childrens.harvard.edu> wrote:

> Hi John,
> Welcome!  There are actually many ways to contribute and it's not limited to just code.
 It's always great to hear new ideas and suggestions on how to improve the software.  Therefore
even, things like user feedback, documentation, new use cases, essentially anything that will
make things better would be awesome!
> To get started, I would suggest subscribing to the email lists.  If you would like to
contribute anything, just create an Jira account (anyone should be able to do this), and add/review
Jira items (add attachments if you like) and we can even help integrate it.
> We normally use Jira to keep track of issues:
> [1] https://issues.apache.org/jira/browse/ctakes
> Current collection of sample test notes that have been collected over the years:
> https://svn.apache.org/repos/asf/ctakes/trunk/ctakes-regression-test/testdata/input/plaintext/
> ________________________________________
> From: Tim Miller [timothy.miller@childrens.harvard.edu]
> Sent: Tuesday, July 02, 2013 6:31 PM
> To: dev@ctakes.apache.org
> Subject: Re: Next cTAKES release (3.1)?
> Agreed that you could definitely help out, and that would be a great way
> to do so. We don't really have "examples" right now, more like just
> short test sentences for showing simple results and verifying that
> nothing has been broken by changes. I think regular length fake but
> realistic notes would be very useful.
> Tim
> On 07/02/2013 05:19 PM, John Green wrote:
>> 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,
>>>> have clearly labeled examples in every module that set up a pipeline, run
>>>> 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
>>>> 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
>>>> 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
>>>> 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,
>>>> have clearly labeled examples in every module that set up a pipeline, run
>>>> 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
>>>>>> request access to it since it is "semi private"
>>>>>> On Jun 27, 2013, at 9:52 PM, vijay garla <vngarla@gmail.com>
>>>>>>> We released code on using cTAKES to annotate clinical text and
>>>>>>> that use the annotations to classify clinical text from the CMC
>>>>>>> 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
>>>>>>> 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
>>>>>>>>> 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
>>>>>>>>> depends
>>>>>> on
>>>>>>>>> lot of other frameworks (UimaFit, cleartk, UIMA Framework
>>>>>>>>> most
>>>>>> of
>>>>>>>>> my spare time is being spent on juggling between these
>>>>>>>> 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
>>>>>>>>> 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
>>>>>> though
>>>>>>>>> training class are there. I understood that there are
>>>>>>>>> issues
>>>>>>>> with
>>>>>>>>> REAL data, but at least some hand made example sentences,
>>>>>>>>> may not
>>>>>>>> be
>>>>>>>>> real but helps developers in understanding the type/structure
>>>>>>>>> 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
>>>>>>>>> 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
>>>>>>>>>>> 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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