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 > >>>>>>> > >