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