> I integrated your ruta scripts and added a new patch (includes and > replaces my last one). > Ok.
> I noticed some semantic differences between the ruta rules and their > jape originals, e.g., the brackets for the user name. Are they intended? > Brackets should be included. I was getting some inconsistent output so I removed them for the time being. > I needed to change some rule elements, e.g, "M.D." does not work as a > literal rule element match (very old restriction of ruta which should be > removed some day...). These literal string matches should be avoided at > all if possible, or at least the start anchor should set to a different > rule element. > OK. > Ok, I'll let you know when I start with a rule set. Great! Azad > Am 20.01.2016 um 01:47 schrieb Azad Dehghan: > > Peter, > > > > So, we have Email, Url, Profession, Street, Zip, State and Username > > completed so far. > > > > The following NERs remain: > > Country, Age, Doctor, Fax, Id_num, Medicalrec_num, Patient, and Phone. > > > > I will do Country next. If you are able to translated the rest quickly > > please do :) else just keep me posted which ones your are working on to > > avoid duplicate work...and we can work through the remaining NERs. > > > > Also, once the NERs are translated I will prepare a number of examples for > > unit testing -- I will also be validate the NERs using the i2b2 research > > dataset. > > > > Cheers, > > Azad > > > > On 19 January 2016 at 09:01, Peter Klügl <peter.klu...@averbis.com> wrote: > > > >> Ok, let me know which ones I should translate. > >> > >> Best, > >> > >> Peter > >> > >> Am 18.01.2016 um 20:13 schrieb Azad Dehghan: > >>> Peter, > >>> > >>> Thanks for pushing things! > >>> > >>> I would rather split the rules/NERs to get things moving quicker (as I > >> am a > >>> newbie to Ruta). I will be uploading another NER (Username) shortly. I > >> will > >>> look at your changes to follow suit. > >>> > >>> Best, > >>> Azad > >>> > >>> On 18 January 2016 at 14:06, Peter Klügl <peter.klu...@averbis.com> > >> wrote: > >>>> Hi, > >>>> > >>>> a new patch is attached. > >>>> > >>>> @Pei: > >>>> are there suitable annotation types in the cTAKES type system? Some > >>>> project in cTAKES uses something like OntologyMatch... I map it to > >>>> IdentifiedAnnotation right now, but there are many empty features... > >>>> > >>>> @Azad: > >>>> I changed the rules a bit, especially the capitalization like I use it > >>>> in ruta normally. The wordlist are compiled to a trie by the maven > >>>> plugin. I also added the two regexes for url and email. I extended the > >>>> regex for the url. I also changed the evaluation order of some rules > >>>> (with @). Feel free to add simple examples to examples.csv for the unit > >>>> tests. > >>>> > >>>> Let me know if you need more information about the changes. > >>>> > >>>> Do you wanna have help with the other rule sets? Or should we split them > >>>> up? > >>>> > >>>> Best, > >>>> > >>>> Peter > >>>> > >>>> Am 18.01.2016 um 11:04 schrieb Peter Klügl: > >>>>> Hi, > >>>>> > >>>>> great. I will integrate them in the project and in the next patch. > >>>>> > >>>>> Best, > >>>>> > >>>>> Peter > >>>>> > >>>>> Am 18.01.2016 um 00:58 schrieb Azad Dehghan: > >>>>>> Three NERs translated and uploaded. > >>>>>> > >>>>>> PS. I will validate all NERs once we have them all completed. > >>>>>> > >>>>>> Cheers, > >>>>>> Azad > >>>>>> > >>>>>> On 24 November 2015 at 10:37, Azad Dehghan <azad.dehg...@gmail.com> > >>>> wrote: > >>>>>>> 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 > >>>>>>>>>>> > >> >
