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 >>>>>>>>>
