CTAKES-384-20160129.patch applied. > On Jan 29, 2016, at 4:34 AM, Peter Klügl <peter.klu...@averbis.com> wrote: > > Hi, > > the problems were caused by the svn client in my Eclipse. Sorry for the > trouble, I should have looked more closely at the ciomplete patch. > > I attached a new patch created with commandline tools wich looks correct > now. > > Pei, can you apply the new patch? > > Best, > > Peter > > Am 28.01.2016 um 15:57 schrieb Peter Klügl: >> Thanks Pei. >> >> I fear there was again a problem with the patch. All new files are >> missing (and also the svn-ignore settings). >> >> Can you take a look? >> >> Best, >> >> Peter >> >> Am 28.01.2016 um 14:43 schrieb Pei Chen: >>> patch applied. >>> Thanks, >>> Pei >>> >>> On Thu, Jan 28, 2016 at 4:14 AM, Peter Klügl <peter.klu...@averbis.com> >>> wrote: >>>> Hi Pei, >>>> >>>> can you commit the recent patch for us? >>>> >>>> CTAKES-384-20160120.patch >>>> >>>> Best, >>>> >>>> Peter >>>> >>>> Am 20.01.2016 um 19:35 schrieb Pei Chen: >>>>> Hi, >>>>> Sorry I was swamped recently. >>>>> But yeah, we can even create an extended type system to store these items >>>>> temporarily and add them into the main/core type system afterwards. >>>>> There was an existing item to upgrade UIMA, but agreed- it will require >>>>> much more testing. If it works, we can upgrade it in our sandbox area or >>>>> create a branch if necessary. >>>>> >>>>> —Pei >>>>> >>>>>> On Jan 18, 2016, at 9:06 AM, 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 >>>>>>>>>>>>> >
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