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 <[email protected]>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 <[email protected]> > 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 <[email protected] > >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" < > [email protected]> > >> 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 > >>> > >> > >> > >
