Hi, sorry, I was quite busy last month.
I added a new patch, which needs to be applied. No new rules, but it's possible now to evaluate everything against the labelled data of the challenge. @Azad: Which documents exactly did you use to develop the rules? training-PHI-Gold-Set1, training-PHI-Gold-Set2 or testing-PHI-Gold-fixed? Best, Peter Am 03.02.2016 um 09:05 schrieb Peter Klügl: > 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 <[email protected]> >>>>> 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 <[email protected]> >>>>>>>> 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 <[email protected]> >>>>>>>>>> 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" <[email protected]> >>>>>>>>>>> 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 >>>>>>>>>>>>> <[email protected]> >>>>>>>>>>> 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 >>>>>>>>>>>>>>>
