ctakes relation extractor

ctakes-relation-extractor

The relation extractor is designed to annotation relations between certain Event, Entity and Modifier annotations.
There are currently models trained for detecting body site and severity using machine learning with a model trained on manually annotated clinical data.

Piper Files

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Piper Files

Default Relation Pipeline

Clinical Pipeline with degree-of and location-of relations.

Default Relation Pipeline

$\textcolor{gray}{\textsf{// Clinical Pipeline with degree-of and location-of relations. }}$

$\textcolor{gray}{\textsf{// Default Clinical Pipeline }}$
$\textcolor{magenta}{\textsf{load}}$ DefaultFastPipeline

$\textcolor{gray}{\textsf{// degree-of, relation-of }}$
$\textcolor{magenta}{\textsf{load}}$ RelationSubPipe

Relation Sub Pipe

Commands and parameters to create a default relation extraction sub-pipeline.

Relation Sub Pipe

$\textcolor{gray}{\textsf{// Commands and parameters to create a default relation extraction sub-pipeline. }}$
$\textcolor{gray}{\textsf{// This is not a full pipeline. }}$

$\textcolor{gray}{\textsf{// Modifiers. Use addLogged to log start and finish of processing. There aren't default models, so set specifically }}$
$\textcolor{green}{\textsf{add}}$ $\textcolor{blue}{\textsf{ModifierExtractorAnnotator}}$ $\textcolor{purple}{\textsf{classifierJarPath}}$= $\textcolor{violet}{\textsf{/org/apache/ctakes/relation/extractor/models/modifier_extractor/model.jar}}$

$\textcolor{gray}{\textsf{// Degree of severity, etc. }}$
$\textcolor{green}{\textsf{add}}$ $\textcolor{blue}{\textsf{DegreeOfRelationExtractorAnnotator}}$ $\textcolor{purple}{\textsf{classifierJarPath}}$= $\textcolor{violet}{\textsf{/org/apache/ctakes/relation/extractor/models/degree_of/model.jar}}$

$\textcolor{gray}{\textsf{// Location. }}$
$\textcolor{green}{\textsf{add}}$ $\textcolor{blue}{\textsf{LocationOfRelationExtractorAnnotator}}$ $\textcolor{purple}{\textsf{classifierJarPath}}$= $\textcolor{violet}{\textsf{/org/apache/ctakes/relation/extractor/models/location_of/model.jar}}$

Sectioned Relation Pipeline

Clinical Pipeline with section, paragraph and list detection and degree-of and location-of relations

Sectioned Relation Pipeline

$\textcolor{gray}{\textsf{// Clinical Pipeline with section, paragraph and list detection and degree-of and location-of relations }}$

$\textcolor{gray}{\textsf{// Default Clinical Pipeline with section, paragraph and list detection }}$
$\textcolor{magenta}{\textsf{load}}$ SectionedFastPipeline

$\textcolor{gray}{\textsf{// degree-of, relation-of }}$
$\textcolor{magenta}{\textsf{load}}$ RelationSubPipe

Ts Default Relation Pipeline

Thread Safe Default Clinical Pipeline with degree-of and location-of relations

Ts Default Relation Pipeline

$\textcolor{gray}{\textsf{// Thread Safe Default Clinical Pipeline with degree-of and location-of relations }}$

$\textcolor{gray}{\textsf{// Default Clinical Pipeline }}$
$\textcolor{magenta}{\textsf{load}}$ TsDefaultFastPipeline

$\textcolor{gray}{\textsf{// degree-of, relation-of }}$
$\textcolor{magenta}{\textsf{load}}$ TsRelationSubPipe

Ts Relation Sub Pipe

Commands and parameters to create a relation extraction sub-pipeline.

Ts Relation Sub Pipe

$\textcolor{gray}{\textsf{// Commands and parameters to create a relation extraction sub-pipeline. }}$
$\textcolor{gray}{\textsf{// This is not a full pipeline. }}$

$\textcolor{gray}{\textsf{// Modifiers. Use addLogged to log start and finish of processing. There aren't default models, so set specifically }}$
$\textcolor{green}{\textsf{add}}$ $\textcolor{blue}{\textsf{concurrent.ThreadSafeModifierExtractor}}$ $\textcolor{purple}{\textsf{classifierJarPath}}$= $\textcolor{violet}{\textsf{/org/apache/ctakes/relation/extractor/models/modifier_extractor/model.jar}}$

$\textcolor{gray}{\textsf{// Degree of severity, etc. }}$
$\textcolor{green}{\textsf{add}}$ $\textcolor{blue}{\textsf{concurrent.ThreadSafeDegreeExtractor}}$ $\textcolor{purple}{\textsf{classifierJarPath}}$= $\textcolor{violet}{\textsf{/org/apache/ctakes/relation/extractor/models/degree_of/model.jar}}$

$\textcolor{gray}{\textsf{// Location. }}$
$\textcolor{green}{\textsf{add}}$ $\textcolor{blue}{\textsf{concurrent.ThreadSafeLocationExtractor}}$ $\textcolor{purple}{\textsf{classifierJarPath}}$= $\textcolor{violet}{\textsf{/org/apache/ctakes/relation/extractor/models/location_of/model.jar}}$

Ts Sectioned Relation Pipeline

Thread Safe Clinical Pipeline with section, paragraph and list detection and degree-of and location-of relations.

Ts Sectioned Relation Pipeline

$\textcolor{gray}{\textsf{// Thread Safe Clinical Pipeline with section, paragraph and list detection and degree-of and location-of relations. }}$

$\textcolor{gray}{\textsf{// Default Clinical Pipeline with section, paragraph and list detection }}$
$\textcolor{magenta}{\textsf{load}}$ TsSectionedFastPipeline

$\textcolor{gray}{\textsf{// degree-of, relation-of }}$
$\textcolor{magenta}{\textsf{load}}$ TsRelationSubPipe