ctakes clinical pipeline

The Default Clinical Pipeline produces the most commonly desired output from cTAKES.
This includes annotations for Anatomical sites, Signs/Symptoms, Procedures, Diseases/Disorders and Medications. For each annotation there are normalized UMLS CUIs, plus values for negation, uncertainty and subject.
The Default ClinicalPipeline is a great place for the new user of a binary installation to start. New developers should look at the ctakes-examples project to start.

Annotation Engines
Piper Files

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Annotation Engines

Extraction Prepper

Assigns IDs and Canonical text to Identified Annotations.

Source class: ExtractionPrepAnnotator
Source package: org.apache.ctakes.clinicalpipeline.ae
Parent class: org.apache.uima.analysis_component.JCasAnnotator_ImplBase
Dependencies: Section, Identified Annotation

No available configuration parameters.

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Piper Files

Default Fast Pipeline

Commands and parameters to create a plaintext document processing pipeline with UMLS entity lookup.

Default Fast Pipeline

$\textcolor{gray}{\textsf{// Commands and parameters to create a plaintext document processing pipeline with UMLS entity lookup. }}$

$\textcolor{gray}{\textsf{// Write nice big banners when ctakes starts and finishes. }}$
$\textcolor{olive}{\textbf{set}}$ $\textcolor{purple}{\textbf{WriteBanner}}$= $\textcolor{violet}{\textsf{yes}}$

$\textcolor{gray}{\textsf{// Load a simple token processing pipeline from another pipeline file }}$
$\textcolor{magenta}{\textbf{load}}$ DefaultTokenizerPipeline

$\textcolor{gray}{\textsf{// Add non-core annotators }}$
$\textcolor{green}{\textbf{add}}$ ContextDependentTokenizerAnnotator
$\textcolor{green}{\textbf{addDescription}}$ POSTagger

$\textcolor{gray}{\textsf{// Add Chunkers }}$
$\textcolor{magenta}{\textbf{load}}$ ChunkerSubPipe

$\textcolor{gray}{\textsf{// Default fast dictionary lookup }}$
$\textcolor{magenta}{\textbf{load}}$ DictionarySubPipe

$\textcolor{gray}{\textsf{// Add Cleartk Entity Attribute annotators }}$
$\textcolor{magenta}{\textbf{load}}$ AttributeCleartkSubPipe

$\textcolor{gray}{\textsf{// Log run time stats and completion }}$
$\textcolor{green}{\textbf{addLast}}$ $\textcolor{blue}{\textsf{util.log.FinishedLogger}}$

Sectioned Fast Pipeline

Commands and parameters to create a plaintext document processing pipeline with Sections, paragraphs and lists.

Sectioned Fast Pipeline

$\textcolor{gray}{\textsf{// Commands and parameters to create a plaintext document processing pipeline with Sections, paragraphs and lists. }}$

$\textcolor{gray}{\textsf{// Advanced Tokenization: Regex sectionization, Paragraphs, Lists }}$
$\textcolor{magenta}{\textbf{load}}$ FullTokenizerPipeline

$\textcolor{gray}{\textsf{// Add non-core annotators }}$
$\textcolor{green}{\textbf{add}}$ ContextDependentTokenizerAnnotator
$\textcolor{green}{\textbf{addDescription}}$ POSTagger

$\textcolor{gray}{\textsf{// Add Chunkers }}$
$\textcolor{magenta}{\textbf{load}}$ ChunkerSubPipe

$\textcolor{gray}{\textsf{// Default fast dictionary lookup }}$
$\textcolor{magenta}{\textbf{load}}$ DictionarySubPipe

$\textcolor{gray}{\textsf{// Add Cleartk Entity Attribute annotators }}$
$\textcolor{magenta}{\textbf{load}}$ AttributeCleartkSubPipe

Ts Default Fast Pipeline

Commands and parameters to create a thread-safe plaintext document processing pipeline with UMLS lookup.

Ts Default Fast Pipeline

$\textcolor{gray}{\textsf{// Commands and parameters to create a thread-safe plaintext document processing pipeline with UMLS lookup. }}$

$\textcolor{gray}{\textsf{// set the thread count }}$
threads 3

$\textcolor{gray}{\textsf{// Load a simple token processing pipeline from another pipeline file }}$
$\textcolor{magenta}{\textbf{load}}$ TsDefaultTokenizerPipeline

$\textcolor{gray}{\textsf{// Add non-core annotators }}$
$\textcolor{green}{\textbf{add}}$ ContextDependentTokenizerAnnotator
$\textcolor{green}{\textbf{addDescription}}$ POSTagger

$\textcolor{gray}{\textsf{// Add Chunkers }}$
$\textcolor{magenta}{\textbf{load}}$ TsChunkerSubPipe

$\textcolor{gray}{\textsf{// Default fast dictionary lookup }}$
$\textcolor{magenta}{\textbf{load}}$ TsDictionarySubPipe

$\textcolor{gray}{\textsf{// Add Cleartk Entity Attribute annotators }}$
$\textcolor{magenta}{\textbf{load}}$ TsAttributeCleartkSubPipe

Ts Sectioned Fast Pipeline

Commands and parameters to create a thread-safe plaintext document processing pipeline with Sections, paragraphs and lists.

Ts Sectioned Fast Pipeline

$\textcolor{gray}{\textsf{// Commands and parameters to create a thread-safe plaintext document processing pipeline with Sections, paragraphs and lists. }}$

$\textcolor{gray}{\textsf{// set the thread count }}$
threads 3

$\textcolor{gray}{\textsf{// Advanced Tokenization: Regex sectionization, Paragraphs, Lists }}$
$\textcolor{magenta}{\textbf{load}}$ TsFullTokenizerPipeline

$\textcolor{gray}{\textsf{// Add non-core annotators }}$
$\textcolor{green}{\textbf{add}}$ ContextDependentTokenizerAnnotator
$\textcolor{green}{\textbf{addDescription}}$ POSTagger

$\textcolor{gray}{\textsf{// Add Chunkers }}$
$\textcolor{magenta}{\textbf{load}}$ TsChunkerSubPipe

$\textcolor{gray}{\textsf{// Default fast dictionary lookup }}$
$\textcolor{magenta}{\textbf{load}}$ TsDictionarySubPipe

$\textcolor{gray}{\textsf{// Add Cleartk Entity Attribute annotators }}$
$\textcolor{magenta}{\textbf{load}}$ TsAttributeCleartkSubPipe