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 >>>>>>>>>>>
