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From: "Savova, Guergana" <Guergana.Savova@childrens.harvard.edu>
To: "dev@ctakes.apache.org" <dev@ctakes.apache.org>
Subject: RE: Next cTAKES release (3.1)?
Thread-Topic: Next cTAKES release (3.1)?
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Date: Thu, 18 Jul 2013 14:24:05 +0000
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Actually, MTsamples is what iDASH downloaded for their notes repository.
--Guergana

-----Original Message-----
From: andy mcmurry [mailto:mcmurry.andy@gmail.com]=20
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 nee=
d 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,=20
> one more year!
>
> - Apropos meds or clinical type questions: any developer on here can=20
> feel free to shoot me a quick question via the list anytime, Id be=20
> happy to confirm that a drug or anything else makes since given a=20
> particular clinical/note context.
>
> - "I wonder if there is someway in which you could guide us in making=20
> better use of the medical knowledge sources (ontologies) that are=20
> available." - I'd be happy to brainstorm about using existing=20
> resources to help in decision making. We use these all the time in the cl=
inic.
>
> @ Tim+Andy+Chen - I haven't had a chance to really start chewing into=20
> the code, though I hope to over the next year; so, what kind of=20
> examples would be most helpful?
>     - Any particular disease processes?
>     - Are you all familiar with the ubiquitous SOAP style presentation=20
> that doctors use to write free notes? The few examples I clicked=20
> through in the repository that Chen pointed me too are very sparse.=20
> Would we want gradations? E.g., a scale for "well done" notes to "very=20
> 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=20
> community in which you hope to integrate. And thank you for pointing=20
> me to the directory with the current sample notes. This was very=20
> helpful in determining where those are at in there development. I know=20
> that each of your hospitals have a wealth of HIPAA-closed notes, but=20
> I'll see what I can do to make some "stereotypical" open-notes for=20
> common disease presentations. Again: maybe a scale, not necessarily=20
> just on brevity but some other metric, whose continuum represented=20
> various permutations of degrees of something, maybe of difficulty in=20
> processing? Apropos code,
> Chen: I will help where I can but where I want to be is elbow deep in=20
> the code :)
>
> Finally: I haven't had a chance to look into some of the links from=20
> earlier in this thread regarding open access repositories of free text=20
> 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 quali=
ty?
>
> Bottom line: no problem either answering contextual questions (can=20
> afib be associated with a lower gi bleed??) and no problem writing=20
> some notes, only question would be, before I put in any time: what diseas=
e/specialty domain?
> and would we want some system that put them on a continuum of some=20
> 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=20
> suggestions on how to improve the software.  Therefore even, things=20
> like user feedback, documentation, new use cases, essentially anything=20
> that will make things better would be awesome!
> >
> > To get started, I would suggest subscribing to the email lists.  If=20
> > you
> would like to contribute anything, just create an Jira account (anyone=20
> should be able to do this), and add/review Jira items (add attachments=20
> 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=20
> > 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=20
> > way to do so. We don't really have "examples" right now, more like=20
> > just short test sentences for showing simple results and verifying=20
> > that nothing has been broken by changes. I think regular length fake=20
> > 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=20
> >> third
> year medical student rounding the bend toward my MD. I used to be a=20
> computer programmer, however, and continue my own projects. Im very=20
> interested in contributing eventually to cTakes development. In the=20
> meantime, given the current talk of examples, if any domain specific=20
> examples needed generated I am domain knowledgable enough that I could=20
> pound out a few free text notes made to order.
> >>
> >> Let me know, you all may already have docs on hand willing todo=20
> >> this,
> but if not...
> >>
> >> John Green
> >>
> >> Sent from my iPhone
> >>
> >> On Jun 28, 2013, at 8:59, "Chen, Pei"=20
> >> <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=20
> some of the areas that need improvements are (which we haven't thought=20
> about earlier).
> >>> I think Tim's suggestions and the 3 concrete actionable items=20
> >>> makes a
> lot of sense.  Hopefully it should attract new users, adopters, and=20
> 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=20
> >>>> pipeline,
> run on
> >>>> sample notes (could be the same sample notes from the tests), and=20
> >>>> do something with the results.
> >>>> iii) Follow Giri's recommendation to have example training data=20
> >>>> 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=20
> pojos;  So the examples could initially shield the complexity of=20
> 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=20
> >>>> [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-=20
> >>>> independent, in the real world it is almost always better to use=20
> >>>> some domain-specific data and we should think more about how to=20
> >>>> facilitate
> that.
> >>>>
> >>>> As for making it easier to get started, it is not totally clear=20
> >>>> to me
> what this
> >>>> means/how to do it so it might be useful to get specific about=20
> >>>> 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)=20
> >>>> UIMAFit
> way than
> >>>> the standard UIMA way of doing things. Is there something we can=20
> >>>> be
> doing
> >>>> to make understanding UIMA easier? Or do we just need to say=20
> >>>> upfront
> that
> >>>> this is a prerequisite and hope that people don't give up due to=20
> >>>> 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=20
> >>>> start
> coding.
> >>>> Pei's GUI will help for some common use cases but will not remove=20
> >>>> the requirement that someone at the organization knows cTAKES.
> >>>> I think one part of this problem is the fact that the typesystem=20
> >>>> is
> not well
> >>>> documented. A developer needs to know what the output is (objects=20
> >>>> from the typesystem), how to get them (which modules/pipelines),=20
> >>>> and what information is in them. So maybe on this end my=20
> >>>> 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=20
> >>>> pipeline,
> run on
> >>>> sample notes (could be the same sample notes from the tests), and=20
> >>>> do something with the results.
> >>>> iii) Follow Giri's recommendation to have example training data=20
> >>>> 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=20
> >>>> 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 han=
d"
> >>>>>
> >>>>> Agree with this statement and this is very valid concern.
> >>>>>
> >>>>> In "getting started examples", I think we should just have=20
> >>>>> couple of entries (5-10 small entries), not more than that (with=20
> >>>>> explicit statement like "ONLY EXAMPLE", NOT GOOD FOR REAL=20
> >>>>> USAGE). I
> >>>> understand
> >>>>> handcrafting these may not be easy because we are not medical=20
> >>>>> domain experts, but I feel worth time, because it brings in more=20
> >>>>> 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=20
> >>>>>> 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=20
> >>>>>>> SVMs that use the annotations to classify clinical text from=20
> >>>>>>> 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=20
> >>>>>>> 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=20
> >>>>>>> code should be reproducible and made publicly available, but=20
> >>>>>>> that's a
> different
> >>>> issue).
> >>>>>>> When we get around to upgrading YTEX to cTAKES 3.1, we would=20
> >>>>>>> like
> to
> >>>>>>> upgrade these samples as well.
> >>>>>>>
> >>>>>>> Best,
> >>>>>>>
> >>>>>>> VJ
> >>>>>>>
> >>>>>>>
> >>>>>>>
> >>>>>>> On Thu, Jun 27, 2013 at 8:32 PM, Andy McMurry=20
> >>>>>>> <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=20
> >>>>>>>> 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=20
> >>>>>>>> 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=20
> >>>>>>>>> features, how
> >>>>>> to,
> >>>>>>>>> etc., which reduces core team work load on documentation.
> >>>>>>>>>
> >>>>>>>>> I have been trying to write a small "how to write standalone=20
> >>>>>>>>> client for ctakes" with my experience (I saw at least 4=20
> >>>>>>>>> users posted similar
> >>>>>>>> question
> >>>>>>>>> in last 2 months), but not getting enough time because=20
> >>>>>>>>> ctakes depends
> >>>>>> on
> >>>>>>>>> lot of other frameworks (UimaFit, cleartk, UIMA Framework=20
> >>>>>>>>> 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=20
> >>>>>>>>> base as
> >>>>>>>> ctakes
> >>>>>>>>> progress), for users I think documentation is lot better=20
> >>>>>>>>> though some improvements need to be done.
> >>>>>>>>>
> >>>>>>>>> As a developer I felt tough with lack of sample training=20
> >>>>>>>>> data (I am
> >>>>>> still
> >>>>>>>>> struggling in this area even though I browsed all relevant=20
> >>>>>>>>> code),
> >>>>>> though
> >>>>>>>>> training class are there. I understood that there are=20
> >>>>>>>>> licensing issues
> >>>>>>>> with
> >>>>>>>>> REAL data, but at least some hand made example sentences,=20
> >>>>>>>>> which may not
> >>>>>>>> be
> >>>>>>>>> real but helps developers in understanding the=20
> >>>>>>>>> type/structure of input TRAINING classes expecting. This way=20
> >>>>>>>>> people who browse the code can
> >>>>>>>> reverse
> >>>>>>>>> engineer and develop their own models. Sorry if you guys=20
> >>>>>>>>> feel
> this
> >>>>>>>>> as novice issue, but I feel most of the developers will be=20
> >>>>>>>>> novice when
> >>>>>> they
> >>>>>>>>> adopt a system and Machine Learning/NLP is ocean. Some=20
> >>>>>>>>> documentation in this area will same lot of time for us.
> >>>>>>>>>
> >>>>>>>>> I wish there will be some activity in this area from ctakes=20
> >>>>>>>>> core
> team.
> >>>>>>>>>
> >>>>>>>>> Thank you,
> >>>>>>>>> Giri
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>> On Thu, Jun 27, 2013 at 5:11 PM, Andy McMurry=20
> >>>>>>>>> <mcmurry.andy@gmail.com
> >>>>>>>>> wrote:
> >>>>>>>>>
> >>>>>>>>>> ctakes is at a point where we have a LOT of features but it=20
> >>>>>>>>>> is still
> >>>>>>>> hard
> >>>>>>>>>> to get started.
> >>>>>>>>>>
> >>>>>>>>>> Judging from the mailing lists a lot of how cTakes works is=20
> >>>>>>>>>> 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=20
> >>>>>>>>>> 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=20
> >>>>>>>>>>> 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=3DfixVersion%20%3D%20%22
> >>>> 3.1%
> >>>>>> 22%20AND%20project%20%3D%20CTAKES
> >
>