Hi, the last patch fixed almost all problems.
I added another one that adds the csv file for the unit test and extends svn-ignore. Best, Peter Am 02.02.2016 um 09:16 schrieb Peter Klügl: > Hi, > > I added another patch. I missed to manually add one test file to version > control, and there are still duplicate lines. > I hope this patch fixes the remaining problems. > > Best, > > Peter > > > Am 29.01.2016 um 10:34 schrieb Peter Klügl: >> 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 >>>>>>>>>>>>>>
