IdentifiedAnnotationUtil

final public class IdentifiedAnnotationUtil

A one-stop shop for the most commonly requested Identified Annotation properties.

• Author: SPF , chip-nlp
• Version: %I%
• Since: 4/21/2020
  
  

static public boolean isRealAffirmed( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation -
• Returns: true iff the annotation is not generic, not uncertain, not negated and not conditional.
  
  

static public Collection<SemanticGroup> getSemanticGroups( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation -
• Returns: Semantic Groups for all Umls Concepts of the annotation
  
  

static public Collection<SemanticTui> getSemanticTuis( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation -
• Returns: Semantic Tuis for all Umls Concepts of the annotation
  
  

static public Collection<String> getCuis( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation -
• Returns: cuis for all Umls Concepts of the annotation
  
  

static public Collection<String> getCodeSchemes( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation -
• Returns: a collection of schemes with codes for the given annotation. e.g. snomed_us, rxnorm.
  
  

static public Collection<String> getCodes( final IdentifiedAnnotation annotation, final String schemeName )

• Parameters:
  • annotation -
  • schemeName the name of a coding scheme. e.g. snomed_us, rxnorm.
• Returns: all annotation codes for the given coding scheme.
  
  

static public Collection<String> getPreferredTexts( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation -
• Returns: preferred texts for all Umls Concepts of the annotation
  
  

static public float getConfidence( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation -
• Returns: the confidence of the annotation
  
  

static public Collection<SemanticGroup> getBestSemanticGroups( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation -
• Returns: the best wsd SemanticGroups
  
  

static public SemanticGroup getBestSemanticGroup( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation -
• Returns: the best wsd SemanticGroups
  
  

static public Collection<SemanticTui> getBestSemanticTuis( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation -
• Returns: the best wsd SemanticTuis
  
  

static public Collection<String> getBestCuis( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation -
• Returns: the best wsd cuis
  
  

static public Collection<String> getBestCodeSchemes( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation -
• Returns: a collection of the best wsd schemes with codes for the given annotation. e.g. snomed_us, rxnorm.
  
  

static public Collection<String> getBestCodes( final IdentifiedAnnotation annotation, final String schemeName )

• Parameters:
  • annotation -
  • schemeName the name of a coding scheme. e.g. snomed_us, rxnorm.
• Returns: the best wsd annotation codes for the given coding scheme.
  
  

static public Collection<String> getBestPreferredTexts( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation -
• Returns: preferred texts for the best wsd Umls Concepts of the annotation