OntologyConceptUtil - apache/ctakes GitHub Wiki

final public class OntologyConceptUtil

  • Author: SPF , chip-nlp
  • Version: %I%
  • Since: 1/8/2015

static public FeatureStructure[] getConceptFeatureStructures( final IdentifiedAnnotation annotation )

  • Parameters:
    • annotation -
  • Returns: array of FeatureStructure castable to array of OntologyConcept

static public Stream<OntologyConcept> getOntologyConceptStream( final IdentifiedAnnotation annotation )

  • Parameters:
    • annotation -
  • Returns: stream of OntologyConcept

static public Collection<OntologyConcept> getOntologyConcepts( final IdentifiedAnnotation annotation )

  • Parameters:
    • annotation -
  • Returns: stream of OntologyConcept

static public Stream<UmlsConcept> getUmlsConceptStream( final IdentifiedAnnotation annotation )

  • Parameters:
    • annotation -
  • Returns: stream of all Umls Concepts associated with the annotation

static public Collection<UmlsConcept> getUmlsConcepts( final IdentifiedAnnotation annotation )

  • Parameters:
    • annotation -
  • Returns: set of all Umls Concepts associated with the annotation

static public Collection<UmlsConcept> getBestUmlsConcepts( final IdentifiedAnnotation annotation )

  • Parameters:
    • annotation -
  • Returns: set of all Umls Concepts associated with the annotation with the highest wsd score

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

  • Parameters:
    • annotation -
  • Returns: set of all Umls cuis associated with the annotation

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

  • Parameters:
    • annotation -
  • Returns: set of all Umls tuis associated with the annotation

static public Map<String, Collection<String>> getSchemeCodes( final IdentifiedAnnotation annotation )

  • Parameters:
    • annotation -
  • Returns: map of ontology scheme names to a set of ontology codes associated each scheme

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

  • Parameters:
    • annotation -
  • Returns: set of ontology codes associated with all schemes

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

  • Parameters:
    • annotation -
    • schemeName name of the scheme of interest
  • Returns: set of ontology codes associated the named scheme

static public Collection<String> getCuis( final JCas jcas )

  • Parameters:
    • jcas -
  • Returns: set of all cuis in jcas

static public Map<String, Long> getCuiCounts( final JCas jcas )

  • Parameters:
    • jcas -
  • Returns: map of all cuis in the jcas and their counts

static public Collection<String> getTuis( final JCas jcas )

  • Parameters:
    • jcas -
  • Returns: set of all tuis in jcas

static public Map<String, Collection<String>> getSchemeCodes( final JCas jcas )

  • Parameters:
    • jcas -
  • Returns: set of all ontology codes in jcas

static public Collection<String> getCodes( final JCas jcas )

  • Parameters:
    • jcas -
  • Returns: set of all ontology codes in jcas

static public Collection<String> getCodes( final JCas jcas, final String schemeName )

  • Parameters:
    • jcas -
    • schemeName name of the scheme of interest
  • Returns: set of ontology codes associated the named scheme

static public Collection<SemanticTui> getSemanticTuis( final JCas jcas )

  • Parameters:
    • jcas -
  • Returns: set of all semantic Types in jcas

static public Collection<SemanticGroup> getSemanticGroups( final JCas jcas )

  • Parameters:
    • jcas -
  • Returns: set of all semantic groups in jcas

static public <T extends Annotation> Collection<String> getCuis( final JCas jcas, final T lookupWindow )

  • Parameters:
    • jcas -
    • lookupWindow -
  • Returns: set of all cuis in lookupWindow

static public <T extends Annotation> Collection<String> getTuis( final JCas jcas, final T lookupWindow )

  • Parameters:
    • jcas -
    • lookupWindow -
  • Returns: set of all tuis in lookupWindow

static public <T extends Annotation> Map<String, Collection<String>> getSchemeCodes( final JCas jcas, final T lookupWindow )

  • Parameters:
    • jcas -
    • lookupWindow -
  • Returns: map of all schemes and their codes in lookupWindow

static public <T extends Annotation> Collection<String> getCodes( final JCas jcas, final T lookupWindow )

  • Parameters:
    • jcas -
    • lookupWindow -
  • Returns: set of all codes in lookupWindow

static public <T extends Annotation> Collection<String> getCodes( final JCas jcas, final T lookupWindow, final String schemeName )

  • Parameters:
    • jcas -
    • lookupWindow -
    • schemeName name of the scheme of interest
  • Returns: set of ontology codes associated the named scheme

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

  • Parameters:
    • annotations -
  • Returns: set of all Umls cuis associated with the annotations

static public Map<String, Long> getCuiCounts( final Collection<IdentifiedAnnotation> annotations )

  • Parameters:
    • annotations -
  • Returns: map of all Umls cuis associated with the annotations and the counts of those cuis

static public Collection<String> getTuis( final Collection<IdentifiedAnnotation> annotations )

  • Parameters:
    • annotations -
  • Returns: set of all Umls tuis associated with the annotation

static public Map<String, Collection<String>> getSchemeCodes( final Collection<IdentifiedAnnotation> annotations )

  • Parameters:
    • annotations -
  • Returns: map of ontology scheme names to a set of ontology codes associated each scheme

static public Collection<String> getCodes( final Collection<IdentifiedAnnotation> annotations )

  • Parameters:
    • annotations -
  • Returns: set of ontology codes associated with all schemes

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

  • Parameters:
    • annotations -
    • schemeName name of the scheme of interest
  • Returns: set of ontology codes associated the named scheme

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

  • Parameters:
    • annotations -
  • Returns: set of Semantic Types associated the named scheme

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

  • Parameters:
    • annotations -
  • Returns: set of ontology codes associated the named scheme

static public Collection<IdentifiedAnnotation> getAnnotationsByCui( final JCas jcas, final String cui )

  • Parameters:
    • jcas -
    • cui cui of interest
  • Returns: all IdentifiedAnnotations that have the given cui

static public Collection<IdentifiedAnnotation> getAnnotationsByTui( final JCas jcas, final String tui )

  • Parameters:
    • jcas -
    • tui tui of interest
  • Returns: all IdentifiedAnnotations that have the given tui

static public Collection<IdentifiedAnnotation> getAnnotationsByCode( final JCas jcas, final String code )

  • Parameters:
    • jcas -
    • code code of interest
  • Returns: all IdentifiedAnnotations that have the given code

static public Collection<IdentifiedAnnotation> getAnnotationsBySemanticTui( final JCas jcas, final SemanticTui tui )

  • Parameters:
    • jcas -
    • tui semantic type of interest
  • Returns: all IdentifiedAnnotations that have the given tui

static public Collection<IdentifiedAnnotation> getAnnotationsBySemanticGroup( final JCas jcas, final SemanticGroup group )

  • Parameters:
    • jcas -
    • group semantic group of interest
  • Returns: all IdentifiedAnnotations that have the given tui

static public Collection<IdentifiedAnnotation> getAnnotationsByCuis( final JCas jcas, final String... cuis )

  • Parameters:
    • jcas -
    • cuis cuis of interest
  • Returns: all IdentifiedAnnotations that have the given tui

static public Collection<IdentifiedAnnotation> getAnnotationsByTuis( final JCas jcas, final String... tuis )

  • Parameters:
    • jcas -
    • tuis tuis of interest
  • Returns: all IdentifiedAnnotations that have the given tui

static public Collection<IdentifiedAnnotation> getAnnotationsByCodes( final JCas jcas, final String... codes )

  • Parameters:
    • jcas -
    • codes codes of interest
  • Returns: all IdentifiedAnnotations that have the given tui

static public Collection<IdentifiedAnnotation> getAnnotationsBySemanticTuis( final JCas jcas, final SemanticTui... tuis )

  • Parameters:
    • jcas -
    • tuis tuis of interest
  • Returns: all IdentifiedAnnotations that have the given tui

static public Collection<IdentifiedAnnotation> getAnnotationsBySemanticGroups( final JCas jcas, final SemanticGroup... groups )

  • Parameters:
    • jcas -
    • groups tuis of interest
  • Returns: all IdentifiedAnnotations that have the given tui

static public <T extends Annotation> Collection<IdentifiedAnnotation> getAnnotationsByCui( final JCas jcas, final T lookupWindow, final String cui )

  • Parameters:
    • jcas -
    • lookupWindow -
    • cui cui of interest
  • Returns: all IdentifiedAnnotations that have the given cui

static public <T extends Annotation> Collection<IdentifiedAnnotation> getAnnotationsByTui( final JCas jcas, final T lookupWindow, final String tui )

  • Parameters:
    • jcas -
    • lookupWindow -
    • tui tui of interest
  • Returns: all IdentifiedAnnotations that have the given tui

static public <T extends Annotation> Collection<IdentifiedAnnotation> getAnnotationsByCode( final JCas jcas, final T lookupWindow, final String code )

  • Parameters:
    • jcas -
    • lookupWindow -
    • code code of interest
  • Returns: all IdentifiedAnnotations that have the given code

static public Collection<IdentifiedAnnotation> getAnnotationsByCui( final Collection<IdentifiedAnnotation> annotations, final String cui )

  • Parameters:
    • annotations annotations for which codes should be found
    • cui cui of interest
  • Returns: all IdentifiedAnnotations that have the given cui

static public Collection<IdentifiedAnnotation> getAnnotationsByTui( final Collection<IdentifiedAnnotation> annotations, final String tui )

  • Parameters:
    • annotations annotations for which codes should be found
    • tui tui of interest
  • Returns: all IdentifiedAnnotations that have the given tui

static public Collection<IdentifiedAnnotation> getAnnotationsByCode( final Collection<IdentifiedAnnotation> annotations, final String code )

  • Parameters:
    • annotations annotations for which codes should be found
    • code code of interest
  • Returns: all IdentifiedAnnotations that have the given code

static public Collection<IdentifiedAnnotation> getAnnotationsBySemanticTui( final Collection<IdentifiedAnnotation> annotations, final SemanticTui tui )

  • Parameters:
    • annotations annotations for which codes should be found
    • tui semantic type of interest
  • Returns: all IdentifiedAnnotations that have the given tui

static public Collection<IdentifiedAnnotation> getAnnotationsBySemanticGroup( final Collection<IdentifiedAnnotation> annotations, final SemanticGroup group )

  • Parameters:
    • annotations annotations for which codes should be found
    • group semantic group of interest
  • Returns: all IdentifiedAnnotations that have the given tui

static public Collection<IdentifiedAnnotation> getAnnotationsByCuis( final Collection<IdentifiedAnnotation> annotations, final String... cuis )

  • Parameters:
    • annotations annotations for which codes should be found
    • cuis cuis of interest
  • Returns: all IdentifiedAnnotations that have the given cui

static public Collection<IdentifiedAnnotation> getAnnotationsByTuis( final Collection<IdentifiedAnnotation> annotations, final String... tuis )

  • Parameters:
    • annotations annotations for which codes should be found
    • tuis tuis of interest
  • Returns: all IdentifiedAnnotations that have the given tui

static public Collection<IdentifiedAnnotation> getAnnotationsByCodes( final Collection<IdentifiedAnnotation> annotations, final String... codes )

  • Parameters:
    • annotations annotations for which codes should be found
    • codes codes of interest
  • Returns: all IdentifiedAnnotations that have the given code

static public Collection<IdentifiedAnnotation> getAnnotationsBySemanticTuis( final Collection<IdentifiedAnnotation> annotations, final SemanticTui... tuis )

  • Parameters:
    • annotations annotations for which codes should be found
    • tuis semantic types of interest
  • Returns: all IdentifiedAnnotations that have the given code

static public Collection<IdentifiedAnnotation> getAnnotationsBySemanticGroups( final Collection<IdentifiedAnnotation> annotations, final SemanticGroup... groups )

  • Parameters:
    • annotations annotations for which codes should be found
    • groups semantic groups of interest
  • Returns: all IdentifiedAnnotations that have the given code
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