ctakes clinical pipeline - apache/ctakes GitHub Wiki
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
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.
Commands and parameters to create a plaintext document processing pipeline with UMLS entity lookup.
$\textcolor{gray}{\textsf{// Commands and parameters to create a plaintext document processing pipeline with UMLS entity lookup. }}$
$\textcolor{gray}{\textsf{// Write nice big banners when ctakes starts and finishes. }}$
$\textcolor{olive}{\textbf{set}}$ $\textcolor{purple}{\textbf{WriteBanner}}$ =$\textcolor{violet}{\textsf{yes}}$
$\textcolor{gray}{\textsf{// Load a simple token processing pipeline from another pipeline file }}$
$\textcolor{magenta}{\textbf{load}}$ 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
$\textcolor{gray}{\textsf{// Log run time stats and completion }}$
$\textcolor{green}{\textbf{addLast}}$ $\textcolor{blue}{\textsf{util.log.FinishedLogger}}$
Commands and parameters to create a plaintext document processing pipeline with Sections, paragraphs and lists.
$\textcolor{gray}{\textsf{// Commands and parameters to create a plaintext document processing pipeline with Sections, paragraphs and lists. }}$
$\textcolor{gray}{\textsf{// Advanced Tokenization: Regex sectionization, Paragraphs, Lists }}$
$\textcolor{magenta}{\textbf{load}}$ 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
Commands and parameters to create a thread-safe plaintext document processing pipeline with UMLS lookup.
$\textcolor{gray}{\textsf{// Commands and parameters to create a thread-safe plaintext document processing pipeline with UMLS lookup. }}$
$\textcolor{gray}{\textsf{// set the thread count }}$
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
Commands and parameters to create a thread-safe plaintext document processing pipeline with Sections, paragraphs and lists.
$\textcolor{gray}{\textsf{// Commands and parameters to create a thread-safe plaintext document processing pipeline with Sections, paragraphs and lists. }}$
$\textcolor{gray}{\textsf{// set the thread count }}$
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