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From "Savova, Guergana" <Guergana.Sav...@childrens.harvard.edu>
Subject RE: Next cTAKES release (3.1)?
Date Thu, 18 Jul 2013 14:24:05 GMT
Actually, MTsamples is what iDASH downloaded for their notes repository.
--Guergana

-----Original Message-----
From: andy mcmurry [mailto:mcmurry.andy@gmail.com] 
Sent: Wednesday, July 03, 2013 7:26 PM
To: dev@ctakes.apache.org
Subject: Re: Next cTAKES release (3.1)?

Mtsamples has lots of free public examples already but we aren't using them yet.  This is
probably because mtsamples don't have the annotations we need to use them as training examples.
On Jul 3, 2013 2:46 PM, "Hephaestus Studio" <hephaestus.studio@gmail.com>
wrote:

> @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
>
> 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/t
> estdata/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, 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#R
> >>>> epr
> >>>> 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%22
> >>>> 3.1%
> >>>>>> 22%20AND%20project%20%3D%20CTAKES
> >
>

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