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 >>>>>>>>>> >
