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From vijay garla <vnga...@gmail.com>
Subject Re: Next cTAKES release (3.1)?
Date Fri, 28 Jun 2013 01:52:43 GMT
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#Reproducing_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/cases/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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