Patch applied: http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-clinical-deid/ <http://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-clinical-deid/> Thanks Peter.
What error did you get with xml-api’s? Do you mean upgrade ctakes to the latest version of uima instead of 2.4.0? —Pei > On Jan 11, 2016, at 12:39 PM, Peter Klügl <peter.klu...@averbis.com> wrote: > > Hi, > > I just added a small patch which adds a maven build process and a dummy > unit test. > > I had some problems with the version of xml-apis. Is this known or > rather a local problem on my build machine? > Is there a reason why cTAKES requires uima 2.4.0? > > Next step would be translating the rules. Azad mentioned that he already > started with that :-) > > Best, > > Peter > > > Am 18.12.2015 um 11:01 schrieb Peter Klügl: >> Hi, >> >> sorry, there was no free time left in December for this issue, but I >> will be able to provide the patches in January (for real). >> >> Best, >> >> Peter >> >> Am 24.11.2015 um 11:37 schrieb Azad Dehghan: >>> This is on my todo list for Dec. as well. If there are any more volunteers >>> for translating JAPE to RUTA, please get in touch. >>> >>> Cheers, >>> Azad >>> >>> On 24 Nov 2015 09:55, "Peter Klügl" <peter.klu...@averbis.com> wrote: >>>> Hi, >>>> >>>> I just wanted to mention that I haven't forgot about it. Unfortunately, >>>> there is just no spare time right now. I hope I will be able to provide >>>> the patches in December. >>>> >>>> Best, >>>> >>>> Peter >>>> >>>> Am 06.11.2015 um 16:40 schrieb Pei Chen: >>>>> Hi Peter, >>>>> I think the ctakes-examples is probably a good starting point at least >>>>> in terms of maven modules, etc. I think it would be good if we use >>>>> uimaFIT style as primary approach to wiring components together and >>>>> generate desc's as secondary... >>>>> I think the actual components that would be required is probably best >>>>> left up to what is actually required for best performing c-deid. The >>>>> output would be interesting, I'm not sure if we should treat this as >>>>> an independent preprocessing component or part of a pipeline (in which >>>>> case, we may need to propose a change to the type system or perhaps an >>>>> alternative JCas view. You can probably open up that discussion to >>>>> the dev group as you see fit.) >>>>> >>>>> My 2 cents... >>>>> >>>>> >>>>> On Fri, Nov 6, 2015 at 3:38 AM, Peter Klügl <peter.klu...@averbis.com> >>> wrote: >>>>>> Hi, >>>>>> >>>>>> Is there a cTAKES project that may serve as an example on how the >>> cTAKES >>>>>> community develops or how a project should look like? >>>>>> I learned that different people set up UIMA project in a quite >>> different >>>>>> manner and I do not what to get inspired by "some sort of out-dated" >>>>>> approach in the cTAKES repo. >>>>>> >>>>>> Are there restriction or preferences about the preprocessing components >>>>>> that should be used and the kind of "output" of the project. >>>>>> Components: On which components may the componetns rely: tokenizer, ... >>>>>> parser, ... dict lookup? >>>>>> "output": Should the project provide a pipeline or a single AE? >>>>>> >>>>>> More comments below. >>>>>> >>>>>> Am 03.11.2015 um 16:54 schrieb Azad Dehghan: >>>>>>>> Who else plans to provide patches for it? Just to avoid duplicate >>> work >>>>>>>> and to coordnate the efforts ... >>>>>>>> >>>>>>> I would like to help with the translating JAPE to RUTA. >>>>>> You can already go ahead with the UIMA Ruta Workbench if you want, or >>>>>> wait until I set up the project with ruta integration. >>>>>> >>>>>> If any questions arise, just ask :-) >>>>>> >>>>>>>> Is there a development dataset which was utilized for the initial >>>>>>>> development, and if yes, is it possible to contribute it too? >>>>>>>> >>>>>>> The data set is unfortunately not publicly available; i2b2 >>>>>>> <https://www.i2b2.org/NLP/DataSets/Main.php> typically releases the >>> data >>>>>>> sets 12 months after a given challenge; this is done on an individual >>> basis >>>>>>> and involve a Data Use Agreement. >>>>>>> >>>>>>> However, I will be able to conduct and coordinate the validation. >>>>>>> >>>>>> Ok, I'll investigate if we have already access to the dataset here. >>>>>> >>>>>> >>>>>>>> My first step would be: >>>>>>>> - set up a maven project >>>>>>>> - set up a development pipeline in a test (with cTAKES components >>>>>>>> replacing the previous ANNIE preprocessing) >>>>>>>> >>>>>>>> >>>>>>>> But one item that we need to review is the 3rd party libs jars that >>>>>>>> were included to ensure compatibility. I’ll be sure to take a look >>> at >>>>>>>> that over the next few weeks. >>>>>>>> >>>>>>>> —Pei >>>>>>>> >>>>>>>> >>>>>>> @Pei - once ANNIE components are replaced there is should not be a >>> need to >>>>>>> worry about the 3rd party libs. >>>>>>> >>>>>>> Also, just a thought: we may want to create an independent component >>> for >>>>>>> the Two Pass recognition (TwoPass.java) as this method have shown >>> useful >>>>>>> for general NER on longitudinal data and surely useful independent of >>> the >>>>>>> deid component. >>>>>>> >>>>>>> >>>>>>> Cheers, >>>>>>> Azad >>>>>>> >
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