How to include my own code library into cTAKES

I want to include ICD10 CA and CCI into cTAKES How to include my own code library into cTAKES so it shows similar to ICD10CM dictionary extracted from UMLS and used within cTAKES?

Re: Build issues today [EXTERNAL]

Is cTAKES 5.0 ready to be used? or is it still under development?where can we download it? On Wednesday, 24 January 2024 at 12:00:07 pm GMT-5, Finan, Sean wrote: Hi Gandhi, Jeff's problem is related to something that avoids the problem that you saw.  You can get rid of your error if

Discrepancy in cTAKES Identification of 'Chemotherapy' SNOMED Codes

Hi AllI wonder if someone can help me answer these questions: I am a PhD student, my research involves utilizing cTAKES. I'm using the desktop version, cTAKES 4.0.0.1 , for my research. I built a dictionary using the most recent SNOMED codes 2023 sourced from UMLS. My research involves using the

Building 2023AA Snomed RxNorm dictionary fails

Hi All I've been working on creating a dictionary for the 2023AA UMLS, specifically incorporating SNOMED and RxNorm. However, I've encountered two main challenges that I'm hoping to get assistance with: 1. Combining SNOMED and RxNorm in Dictionary Creation:   To initiate the process, I extracted

Re: Discussion on Apache UIMA Ruta (Rule-based Text Annotation) [EXTERNAL] [SUSPICIOUS] [SUSPICIOUS]

Please send me an invitation as...@yahoo.com On Wednesday, 26 May 2021, 05:19:54 am GMT-7, Finan, Sean wrote: BTW, I have created a new meeting and the invitation below is defunct.  You still need to email me with your info to get an invitation. Sean ___

Re: "No piper file found for ChunkerSubPipe" on debug [EXTERNAL]

ui.java:53) Process finished with exit code 1 Any idea how to resolve that? On Monday, 15 February 2021, 06:50:09 am GMT-8, Monogyiou, Eugenia wrote: Hi Akram, If you update from the trunk you must be able to locate this : \ctakes-gui\src\main\java\org\apache\ctakes\gu

Re: "No piper file found for ChunkerSubPipe" on debug [EXTERNAL]

: Hi Akram, I think that the problem is your classpath. When you run a main(..) class in intellij, it uses the classpath of the module in which that class lies. For the PIperRunnerGui it uses the classpath of ctakes-gui. ctakes-gui does not have any dependency upon modules such as

cTAKES to move files after it finishes

Hi All.. The new version of cTAKES cTAKES runs perfectly fine. Sometime I have to stop cTAKES in the middle for some reason and when I re-run it again it starts all over and re-do same files were done already. I wonder if there is a method/config/command that force cTAKES to move finished files t

Error when building executable cTAKES

Hi All I am trying to deploy cTAKES code, and generate Jar files so I can execute code through commands What I did is I tried to Run the "deploy" option in Maves > Apache cTAKES > Lifecycle > deploy I also tried the installatioin option "install" in Maves > Apache cTAKES > Lifecycle > install

Generate Installation files from source code

Hi Everyone I have a technical question I know that We can download cTAKES installation files and cTAKES source code. I made few changes to cTAKES code and tried to put the changes in the installtion folder. I got these problems. 1- I am getting this error when I try to deploy (I want to deploy i

Re: Authentication update

Thanks Peter, Is there a way we can use cTAKES completely offline? I mean we can download whatever we need from UMLS and use it as datasource locally in our computers? On Thursday, 24 September 2020, 02:02:15 pm GMT-7, Peter Abramowitsch wrote: Hi All I managed to have a conversati

Re: Current thinking on new UMLS authentication

Does that mean cTAKES is not going to work? My PhD research depends on it. Is there anyway we can get cTAKES working without the need to authenticate UMLS? as Gres suggested, can we just download NLM model and use cTAKES offline compeletely? Thanks On Friday, 18 September 2020, 10:46:12 am

MS SQL, ytex and ctakes

Hi All.. I have been searching for a while trying to find a way to read and write into MS SQL Server database using cTAKES 1- Instead of reading for text file, I am trying to make cTAKES read from SQL Server DB. 2- instead of writing XMI results into a text file,   I am trying to make cTAKES wri

Re: using UMLS Metathesaurus in cTAKES offline [EXTERNAL]

s and simpler usage for everybody. Of course, private funding would also help ... Sean From: Peter Abramowitsch Sent: Sunday, May 24, 2020 2:49 AM To: dev@ctakes.apache.org; Akram Subject: Re: using UMLS Metathesaurus in cTAKES offline [EXTERNAL

using UMLS Metathesaurus in cTAKES offline

I want to use cTAKES offline I am using command line      run\runClinicalPipeline  -i E:\cTAKES\files\MedReps\Input  --xmiOut E:\cTAKES\files\MedReps\Output  --user myuser  --pass mypassword This is my piper file  load DefaultTokenizerPipeline.piper add DefaultJCasTermAnnotator load Attribut

how to activate inactive features in cTAKES?

Hi  I can extract many tags when I use the default .piper in cTakes  Tags such as LabMention, AnatomicalSiteMention, ProcedureMention, etc they all extracted from applying this piper load DefaultTokenizerPipeline load DictionarySubP

Generating ICD10 without Tokenizing

Hi This is how my .piper look like load DefaultTokenizerPipeline load DictionarySubPipe writeHtmlwriteXmis It works fine and I get these tags in .XMI file after running runPiperGui SentenceWordTokenPunctuationTokenSymbolTokenNumTokenContractionToken also these tags MedicationMentionDiseaseDisorder

Re: Using UMLS full dictionary in cTakes [EXTERNAL]

  I found one of Sean's emails in the Archive the answer for my question aparently I have to copy ICD10 folder and ICD10.xml into the resource folder [cTAKES home]\resources\org\apache\ctakes\dictionary\lookup\fast Thanks Sean :) On Sunday, 29 December 2019, 04:16:36 pm AEDT, Akram

Re: Using UMLS full dictionary in cTakes [EXTERNAL]

I am having similar issue. I created a Dictionary through dictionary creator gui I got a folder called ICD10 and an XML file called ICD10.XML in  J:\cTAKES\ctakes-dictionary-lookup-fast-res\target\classes\org\apache\ctakes\dictionary\lookup\fast I am using the default piper DefaultFastPipeline.

Re: "No piper file found for ChunkerSubPipe" on debug [EXTERNAL]

  ChunkerSubPipe.piper I tried to install cTAKES on 2 different computers and got same issue on both. it only happens when I run from PiperRunnerGui (same as the image attached)  No problems if I use Profilers On Monday, 23 December 2019, 4:54:05 am AEDT, Finan, Sean wrote: ​Hi Akram, I

"No piper file found for ChunkerSubPipe" on debug

I followed Sean's instructions to run "runPiperGUI" from Profiles using "DefaultFastPipeline_Test.piper" file works perfectly. I tried to debug the process ( I will do some changes later ) I run "PiperRunnerGUI"  using "DefaultFastPipeline_Test.piper" file but I get this error ! "No piper file fo

Re: How does cTAKES work? [EXTERNAL]

provided text. Then we save the results as .XMI which can be taken to any tool suck as UIMA to display results visually am I right here? Thanks On Tuesday, 17 December 2019, 02:54:03 am AEDT, Finan, Sean wrote: Hi Akram, Gandhi has provided some good links, and I agree that you sho

Re: How does cTAKES work?

impl       initialize      165              org.apache.uima.impl.AnalysisEngineFactory_impl      produceResource      94    On Sunday, 15 December 2019, 05:46:24 pm AEDT, gandhi rajan wrote: Hi Akram, I would prefer to have a look at the following link: https://cwiki.apache.org/confluence/

How does cTAKES work?

Hi I have 2 questions, and would appreciate the help. The first question == I have been trying to get how cTAKES work and not so much luck I know that we build .piper file through "cTAKES Simple Pipeline Fabricator" we get a .piper file Then the process is not clear my understanding

Re: ctakes gui [EXTERNAL]

wrote: Hi Akram, That was never released with ctakes.  It is in ctakes sandbox as a "proof of concept" project. https://svn.apache.org/repos/asf/ctakes/sandbox/ctakes-gui/ The original author Pei Chen might be able to say more. It has nothing to do with the released "cta

ctakes gui

Hi I have been trying to get ctakes GUI working as the instructions in herehttps://community.i2b2.org/wiki/display/NLPCTAKES/NLP+cTakes+Home I could not find any website that has ctakesgui.war I thought it must be the same project in ctakes open source which is ctakes-gui  but this project ctake

Installing cTAKES on Windows 10

I have been trying to install cTAKES for 2 weeks on Windows 10 through IntelliJ and Eclipse with no luck cTAKES is the core of my NLP research. I have followed the instuctions in this page step by step but it does not work.these steps are either for an older version or missing somthing or some

Re: confirm subscribe to dev@ctakes.apache.org

V2o6Tu02DDUE3qQrQ7UIANYecoLStU _cjwU5Rm4BW3dQWP_Qjjcn1CVORxjL9lMDxeeohwtNbEdLm_f2kEahfWDHWCImVjjSu6.K8iH8yh TRt7KzlHjZZK.V8L_n6jAf8UNaiiMcA-- Received: from sonic.gate.mail.ne1.yahoo.com by sonic316.consmr.mail.ne1.yahoo.com with HTTP; Sat, 7 Dec 2019 05:00:41 + Date: Sat, 7 Dec 2019