iDash and others have medical NLP datasets that could be used for ctakes "Getting Started" examples http://idash.ucsd.edu/nlp-and-data-modeling http://idash.ucsd.edu/nlp/umls-vm
the GOOD: iDash already includes ctakes the BAD: iDash references old versions ctakes and points to cabig (which is now defunct) Recommendation: we should talk to iDash, create "hello medical world" training examples, and request iDaash point to the cTakes Apache home page. Disclaimer: I'm not involved with iDash On Jun 27, 2013, at 10:58 PM, Girivaraprasad Nambari <girinamb...@gmail.com> 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.a...@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 <vnga...@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#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.a...@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 < >> girinamb...@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.a...@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.c...@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 >>>>>>> >>>>>> >>>>>> >>>> >>>> >> >>
