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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

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46 questions
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using cTAKES to parse clinical documents

I am trying to figure out how to run the Clinical Document Pipeline from Java. I have a set of clinical documents as plain texts. I want to parse these documents and extract a list of that is in document doc_ID, there is CUI with frequency of…
user2600417
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How do I add a new dictionary database to cTAKES

How do I add a new database to the cTAKES pipeline to perform lookup from? How do I specify what columns to look up and how to annotate the text with the returned hits? I have gone through the DictionaryLookupAnnotatorDB.xml and LookupDesc_Db.xml…
supriyo_basak
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How to use cTAKES from the command line?

I wonder how to use Apache cTAKES from the command line. E.g. : I have a file note.txt that contains some text like "Patient had elevated blood sugar but tests confirm no diabetes. Patient's father had adult onset diabetes." I want to use the…
Franck Dernoncourt
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Apache cTAKES logic from Java application

I'm trying to embed Apache cTAKES NLP logic into my application. First of all, I'm unable to find any good documentation in order to be educated how it can be done. From the different pieces of code that I found on the internet I have created the…
alexanoid
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tool to convert pre-cordinated SNOMED to post-coordinated

I have typed into the international Snomed browser tool `Superficial injury of head" to which I get the following…
brucezepplin
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Sample code to use cTakes AggregatePlaintextUMLSProcessor

I'm new to Java and UIMA, and I can't find a comprehensive sample to use the AggregatePlaintextUMLSProcessor from code and print results in a proper format. I managed to run cTakes from command line and I see it's using FileWriterCasConsumer.xml to…
Mokhtar Ashour
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integrating independent ontology into UIMA based cTAKES

Okay, so basically, I have a cTAKES pipeline that makes use of the UMLSlookupannotator to perform NER (named entity recognition). Additionally I have a .owl ontology that I have made using protege. Essentially, what I am trying to do is to extend…
jdv12
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Servlet.init() for servlet ctakes-rest-service threw exception

I am a beginner to programming. I am trying to run ctakes API in windows version but getting the following errors when I am trying to get response through Postman. Could anyone please guide me towards correct steps? Thanks in…
Al Jawad Nafad
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java.sql.SQLSyntaxErrorException: user lacks privilege or object not found in ubuntu

I have found many similar questions on internet and tried many solutions but still can't get around this error even after 10 hours. So please give ANY suggestion before marking it as a duplicate. I am also not familiar with hsqldb so please let me…
whoosis
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cTAKES 4, custom dictionary, CAS Visual Debugger (CVD) and AggregatePlaintextFastUMLSProcessor.xml

I was able to install cTAKES 4 with the following documentation https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+-+Fast+Dictionary+Lookup On my Windows 10 machine I run the CAS Visual Debugger (CVD) application via the following…
alexanoid
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Can't retrieve data back from UMLS

I have been trying to run the ctakes-temporal-demo on github. Currently I have configured everything in eclipse correctly. I have set the correct password and id for UMLS account. When I try to run it I get the following error: Exception in thread…
daredevil11
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Getting output in JSON format in UIMA

I'm using Apache cTAKES where the output is required in JSON. I'm trying google's gson here, public static void main(final String... args) throws IOException, UIMAException, SAXException { final String note = "Serum Cholesterol 154 150 250…
moinsy
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cTAKES parser output

I am trying to understand the result generated via cTAKES parser. I am unable to understand certain points- cTAKES parser is invoked via TIKa-app we get following result- ctakes:AnatomicalSiteMention:…
blueiris
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Adding custom writer in apache ctakes

I have checked-out ctakes-4.0.0 (https://codeload.github.com/apache/ctakes/zip/ctakes-4.0.0) and setup in my local machine. I have setup the pipeline for a particular requirement as below load DefaultTokenizerPipeline.piper add…
User_1940878
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how to get ctakes gui running while the ctakes-gui does not have any jsp file?

I Have been following this instructions of ctakes GUI link here https://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…
asmgx
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