Hello Sean Finan, Hope your vacation was great. I have tried to go through all the resources you provided in your last email. I understood some of the parts of cTAKES but I am still not bale to crack how to analyse a clinical note using cTAKES - load a file, apply different annotators, how to modify descriptors using CPE.
Currently, I am able to create a piper file, validate it but I am unable to run it. I am getting a null pointer and other exceptions. Also, the links say that cTAKES should have some default inbuilt piper files although I was not able to find these files. It is a confusion right now on how to use all the interfaces for processing of clinical notes. I believe that since I am new to the software I am having a difficulty connecting the dots and hence unable to get cTAKES to run successfully and be able to make the most of it. Any more resources or say, a user manual would be very helpful. On Thu, Apr 26, 2018 at 11:03 PM, Lohitaksh Yogi <ly...@uncc.edu> wrote: > Hello Sean, thank you for the prompt reply. This is so kind of you. Thank > you for the help. I will go through with these link. > > > > > > On Wed, Apr 25, 2018 at 10:36 AM, Finan, Sean < > sean.fi...@childrens.harvard.edu> wrote: > >> Hi Lohitaksh Yogi, >> >> Wow, I wish that you had asked 2 weeks ago as I was actually working in >> Charlotte for the week. I could have met you on-site. >> >> There is a small pamphlet available that might help. Visit >> https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0 >> and click the second link under Documentation: >> A pamphlet/manual on cTAKES basics >> >> That might help a little bit. I don't use Eclipse myself, but plenty of >> people on the user list and dev list do. You could send questions to >> u...@ctakes.apache.org or dev@ctakes.apache.org: >> https://ctakes.apache.org/mailing-lists.html >> >> If you are using the developer version (trunk), you can enable the maven >> profile to start the gui. It is something like "startGui" ... I don't have >> it in front of me right now, but Eclipse should have the ability to list >> available profiles. https://cwiki.apache.org/confl >> uence/display/CTAKES/Piper+File+Submitter+GUI >> Piper files are all in ctakes-***-res modules under directories named >> pipeline/. The default clinical pipeline is in >> ctakes-clinical-pipeline-res/..../pipeline/ I think that it is called >> "DefaultFastPipeline.piper" or something like that. >> >> I am actually on vacation right now, but if you can wait until next week >> I would be happy to provide more help. >> >> Sean >> ________________________________________ >> From: Lohitaksh Yogi <ly...@uncc.edu> >> Sent: Tuesday, April 24, 2018 9:59 PM >> To: dev@ctakes.apache.org >> Subject: Request for assistance with cTAKES [EXTERNAL] >> >> Hello Sean Finan, >> >> I am a Graduate Student and Research Assistant at UNC Charlotte with Prof >> Ge. We are currently working on the analysis of Clinical Notes using NLP. >> I >> am trying to use cTAKES for the same. >> >> Till now I have followed the instructions to install cTAKES in Eclipse. >> All >> the libraries for NLP have been loaded in Eclipse. I plan to use i2b2 >> dataset 2014 challenge and run it in cTAKES with Eclipse. Could you please >> help me with a manual or instructions to run cTAKES using Eclipse. A demo >> or an example would be helpful since there are very fewer resources >> available on the internet which would guide users through it. >> >> PS: Instructions followed from 'https://urldefense.proofpoint >> .com/v2/url?u=https-3A__cwiki.apache.org_&d=DwIFaQ&c= >> qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpy >> IisCYNYmQCP6r0bcpKGd4f7d4gTao&m=6r_kaMPxweoawRWBk7vwkWIJEzjo >> gYem6PyCxxX221w&s=9PfpRCTeUTW5tu6bsLglGrys8UtkMW2ZNOmYgR9FXsc&e= >> confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide >> <https://urldefense.proofpoint.com/v2/url?u=https-3A__cwiki.apache.org_&d=DwIFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=fs67GvlGZstTpyIisCYNYmQCP6r0bcpKGd4f7d4gTao&m=6r_kaMPxweoawRWBk7vwkWIJEzjogYem6PyCxxX221w&s=9PfpRCTeUTW5tu6bsLglGrys8UtkMW2ZNOmYgR9FXsc&e=confluence/display/CTAKES/cTAKES+4.0+Developer+Install+Guide> >> ' >> -- >> Thanks & Regards >> Lohitaksh Yogi >> >> > > > > -- > Thanks & Regards > Lohitaksh Yogi > -- Thanks & Regards Lohitaksh Yogi
