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 >>>>>>>>>>>>
