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From John Green <hephaestus.stu...@gmail.com>
Subject Re: Next cTAKES release (3.1)?
Date Wed, 03 Jul 2013 13:13:21 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 quality?

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,

Thanks,
JG


On Tue, Jul 2, 2013 at 6:30 PM, Tim Miller <
timothy.miller@childrens.harvard.edu> wrote:

> 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<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<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<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<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<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<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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