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Questions tagged [ctakes]

Apache cTAKES is a natural language processing system for extraction of information from electronic medical record clinical free-text.

cTAKES is a natural language processing system for extraction of information from electronic medical record clinical free-text. Originally developed at the Mayo Clinic, it has expanded to being used by various institutions internationally.

The best way to get started with using cTAKES is to check out the Apache cTAKES confluence

Useful links:

Demos

Examples

Issue tracker

Mailing lists

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How to fix this error Cannot run program "svn" Error in Java

I have problem loading open source application I have followed these steps Perform a fresh checkout from SVN 1. Start IntelliJ IDEa. 2.In the "Quick Start" menu, select "Check out from Version Control". This will display a drop-down box. 3.In the…
asmgx
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Running Java based open source

This is my first time to use Java, and I have no experience in Java, but good experience in .Net I have downloaded an open source code called ctakes and downloaded IntelliJ IDE community version i pointed to the main folder of the project to be…
asmgx
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Why isn't Ctakes able to identify : 'colorectal cancer' medical text in spite of using 'ContextDependentTokenizerAnnotator'?

Ctakes is able to identify 'lung cancer' , 'basal cell cancer' and such - that is it gives a proper SNOMED UMLS identifier. But if the sentence contains colorectal cancer, it just return 'malignant neeplasm' I have tried playing around with…
Yash
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What exactly are the UMLS and SNOMED-CT vocabularies used by cTAKES?

Very new to cTAKES and looking through the docs, curious about what exactly the UMLS and SNOMEDCT "vocabularies" are. The user installation docs don't really seem to tell and simply applying for the UMLS license and the language around the UMLS…
lampShadesDrifter
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How to revise CVD and CPE of Ctakes to access UMLS?

I am a new user for cTakes. When installation, I met with difficulties in adding UMLS username and password to Ctakes. The CPU field showed that C:\Users\Administrator>cd \apache-ctakes-4.0.0 C:\apache-ctakes-4.0.0>bin\runctakesCVD.bat …
yuan
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Using cTakes with UIMA in Java code eclipse

I am trying to do NLP using cTAKES in Eclipse. I have followed the official developers guide for installing cTAKES in Eclipse but I couldnt find any documentation of what to do next i.e how would I import cTAKES pipelines or analysisengine etc. in…
whoosis
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CTakes with Tika

Has anyone integrated ctakes parser with Tika , I would like to use Tika to extract text from documents and use ctakes to get annotations . I’m able to extract using Tika the text and some metadata but would like some advise / help on how to…
RData
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cTakes taking an extremely long time on 'MaxentParserWrapper - Starting Processing: .DS_Strore'

I am trying to run cTakes and use the CPE implementation. I've followed the User Guide exactly, but when I run it (press the 'go' arrow) the process seems to get stuck on 'MaxentParserWrapper - Starting Processing: .DS_Strore' for a very long time.…
Biscuit
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Does anyone know whether Apache Ctakes can run UMLS without internet connection?

Does anyone know whether Apache Ctakes can run UMLS without internet connection and whether there is a good Python wrapper around Ctakes ?
Benjamin Chong
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cTAKES UMLS ICD10 codes lookup

I created a cTAKES custom dictionary from UMLS database with ICD10 codes. Right now I able to analyze the text by for example disease name, like Asthma and annotation index will contain the ICD10 code for this matching code = "J45.90". Is it…
alexanoid
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Check validity of UMLS licence in UmlsDictionaryLookupAnnotator

In UmlsDictionaryLookupAnnotator there is a function isValidUMLSUser having four parameters. In which two of them are username and pass which i have entered correctly but other two are license code and url. Can anyone help me out to find the correct…
ritwik
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Spark Throwing a "NoClassDefFoundError" Despite jar Indicating Class is Present

I am receiving a NoClassDefFoundError despite 7Zip indicating the jar containing the class is present in the uberjar being submitted to run the program. I am submitting with the below line: spark-submit --class…
mongolol
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executing CTAKES NLP through eclipse

I had tried to execute Ctakes NLP class CTAKESClinicalPipelineFactory class but got following error: java.lang.ClassCastException: class org.cleartk.classifier.liblinear.LIBLINEARStringOutcomeClassifierBuilder
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cTAKES and Thread Safety

I am facing issues on cTAKES (An apache project) with respect to thread safety while using the AnalysisEngine and JCAS. I tried getting resolution regarding the same on the Question/Answer on Apache project but not getting sufficient info. If anyone…
Paresh Nakum
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How do I install the cTAKES in eclipse IDE?

I want to install the cTAKES in eclipse but did not find any proper documentation. I am following the documentation of Apache software foundation but I am not able to install cTAKES. Please suggest any proper method to install.
Brijesh Prajapati
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