org.apache.ctakes.core.util

Class OntologyConceptUtil

java.lang.Object

org.apache.ctakes.core.util.OntologyConceptUtil

public final class OntologyConceptUtil
extends Object

Since:

1/8/2015

Version:

%I%

Author:

SPF , chip-nlp

Method Summary

Modifier and Type	Method and Description
static Collection<IdentifiedAnnotation>	getAnnotationsByCode(Collection<IdentifiedAnnotation> annotations, String code)
static Collection<IdentifiedAnnotation>	getAnnotationsByCode(org.apache.uima.jcas.JCas jcas, String code)
static <T extends org.apache.uima.jcas.tcas.Annotation> Collection<IdentifiedAnnotation>	getAnnotationsByCode(org.apache.uima.jcas.JCas jcas, T lookupWindow, String code)
static Collection<IdentifiedAnnotation>	getAnnotationsByCui(Collection<IdentifiedAnnotation> annotations, String cui)
static Collection<IdentifiedAnnotation>	getAnnotationsByCui(org.apache.uima.jcas.JCas jcas, String cui)
static <T extends org.apache.uima.jcas.tcas.Annotation> Collection<IdentifiedAnnotation>	getAnnotationsByCui(org.apache.uima.jcas.JCas jcas, T lookupWindow, String cui)
static Collection<IdentifiedAnnotation>	getAnnotationsByTui(Collection<IdentifiedAnnotation> annotations, String tui)
static Collection<IdentifiedAnnotation>	getAnnotationsByTui(org.apache.uima.jcas.JCas jcas, String tui)
static <T extends org.apache.uima.jcas.tcas.Annotation> Collection<IdentifiedAnnotation>	getAnnotationsByTui(org.apache.uima.jcas.JCas jcas, T lookupWindow, String tui)
static Collection<String>	getCodes(Collection<IdentifiedAnnotation> annotations)
static Collection<String>	getCodes(Collection<IdentifiedAnnotation> annotations, String schemeName)
static Collection<String>	getCodes(IdentifiedAnnotation annotation)
static Collection<String>	getCodes(IdentifiedAnnotation annotation, String schemeName)
static Collection<String>	getCodes(org.apache.uima.jcas.JCas jcas)
static Collection<String>	getCodes(org.apache.uima.jcas.JCas jcas, String schemeName)
static <T extends org.apache.uima.jcas.tcas.Annotation> Collection<String>	getCodes(org.apache.uima.jcas.JCas jcas, T lookupWindow)
static <T extends org.apache.uima.jcas.tcas.Annotation> Collection<String>	getCodes(org.apache.uima.jcas.JCas jcas, T lookupWindow, String schemeName)
static org.apache.uima.cas.FeatureStructure[]	getConceptFeatureStructures(IdentifiedAnnotation annotation)
static Map<String,Long>	getCuiCounts(Collection<IdentifiedAnnotation> annotations)
static Map<String,Long>	getCuiCounts(org.apache.uima.jcas.JCas jcas)
static Collection<String>	getCuis(Collection<IdentifiedAnnotation> annotations)
static Collection<String>	getCuis(IdentifiedAnnotation annotation)
static Collection<String>	getCuis(org.apache.uima.jcas.JCas jcas)
static <T extends org.apache.uima.jcas.tcas.Annotation> Collection<String>	getCuis(org.apache.uima.jcas.JCas jcas, T lookupWindow)
static Collection<OntologyConcept>	getOntologyConcepts(IdentifiedAnnotation annotation)
static java.util.stream.Stream<OntologyConcept>	getOntologyConceptStream(IdentifiedAnnotation annotation)
static Map<String,Collection<String>>	getSchemeCodes(Collection<IdentifiedAnnotation> annotations)
static Map<String,Collection<String>>	getSchemeCodes(IdentifiedAnnotation annotation)
static Map<String,Collection<String>>	getSchemeCodes(org.apache.uima.jcas.JCas jcas)
static <T extends org.apache.uima.jcas.tcas.Annotation> Map<String,Collection<String>>	getSchemeCodes(org.apache.uima.jcas.JCas jcas, T lookupWindow)
static Collection<String>	getTuis(Collection<IdentifiedAnnotation> annotations)
static Collection<String>	getTuis(IdentifiedAnnotation annotation)
static Collection<String>	getTuis(org.apache.uima.jcas.JCas jcas)
static <T extends org.apache.uima.jcas.tcas.Annotation> Collection<String>	getTuis(org.apache.uima.jcas.JCas jcas, T lookupWindow)
static Collection<UmlsConcept>	getUmlsConcepts(IdentifiedAnnotation annotation)
static java.util.stream.Stream<UmlsConcept>	getUmlsConceptStream(IdentifiedAnnotation annotation)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getConceptFeatureStructures

public static org.apache.uima.cas.FeatureStructure[] getConceptFeatureStructures(IdentifiedAnnotation annotation)

Parameters:

annotation - -

Returns:

array of FeatureStructure castable to array of OntologyConcept

getOntologyConceptStream

public static java.util.stream.Stream<OntologyConcept> getOntologyConceptStream(IdentifiedAnnotation annotation)

Parameters:

annotation - -

Returns:

stream of OntologyConcept

getOntologyConcepts

public static Collection<OntologyConcept> getOntologyConcepts(IdentifiedAnnotation annotation)

Parameters:

annotation - -

Returns:

stream of OntologyConcept

getUmlsConceptStream

public static java.util.stream.Stream<UmlsConcept> getUmlsConceptStream(IdentifiedAnnotation annotation)

Parameters:

annotation - -

Returns:

stream of all Umls Concepts associated with the annotation

getUmlsConcepts

public static Collection<UmlsConcept> getUmlsConcepts(IdentifiedAnnotation annotation)

Parameters:

annotation - -

Returns:

set of all Umls Concepts associated with the annotation

getCuis

public static Collection<String> getCuis(IdentifiedAnnotation annotation)

Parameters:

annotation - -

Returns:

set of all Umls cuis associated with the annotation

getTuis

public static Collection<String> getTuis(IdentifiedAnnotation annotation)

Parameters:

annotation - -

Returns:

set of all Umls tuis associated with the annotation

getSchemeCodes

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

Parameters:

annotation - -

Returns:

map of ontology scheme names to a set of ontology codes associated each scheme

getCodes

public static Collection<String> getCodes(IdentifiedAnnotation annotation)

Parameters:

annotation - -

Returns:

set of ontology codes associated with all schemes

getCodes

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

Parameters:

annotation - -

schemeName - name of the scheme of interest

Returns:

set of ontology codes associated the named scheme

getCuis

public static Collection<String> getCuis(org.apache.uima.jcas.JCas jcas)

Parameters:

jcas - -

Returns:

set of all cuis in jcas

getCuiCounts

public static Map<String,Long> getCuiCounts(org.apache.uima.jcas.JCas jcas)

Parameters:

jcas - -

Returns:

map of all cuis in the jcas and their counts

getTuis

public static Collection<String> getTuis(org.apache.uima.jcas.JCas jcas)

Parameters:

jcas - -

Returns:

set of all tuis in jcas

getSchemeCodes

public static Map<String,Collection<String>> getSchemeCodes(org.apache.uima.jcas.JCas jcas)

Parameters:

jcas - -

Returns:

set of all ontology codes in jcas

getCodes

public static Collection<String> getCodes(org.apache.uima.jcas.JCas jcas)

Parameters:

jcas - -

Returns:

set of all ontology codes in jcas

getCodes

public static Collection<String> getCodes(org.apache.uima.jcas.JCas jcas,
                                          String schemeName)

Parameters:

jcas - -

schemeName - name of the scheme of interest

Returns:

set of ontology codes associated the named scheme

getCuis

public static <T extends org.apache.uima.jcas.tcas.Annotation> Collection<String> getCuis(org.apache.uima.jcas.JCas jcas,
                                                                                          T lookupWindow)

Parameters:

jcas - -

lookupWindow - -

Returns:

set of all cuis in lookupWindow

getTuis

public static <T extends org.apache.uima.jcas.tcas.Annotation> Collection<String> getTuis(org.apache.uima.jcas.JCas jcas,
                                                                                          T lookupWindow)

Parameters:

jcas - -

lookupWindow - -

Returns:

set of all tuis in lookupWindow

getSchemeCodes

public static <T extends org.apache.uima.jcas.tcas.Annotation> Map<String,Collection<String>> getSchemeCodes(org.apache.uima.jcas.JCas jcas,
                                                                                                             T lookupWindow)

Parameters:

jcas - -

lookupWindow - -

Returns:

map of all schemes and their codes in lookupWindow

getCodes

public static <T extends org.apache.uima.jcas.tcas.Annotation> Collection<String> getCodes(org.apache.uima.jcas.JCas jcas,
                                                                                           T lookupWindow)

Parameters:

jcas - -

lookupWindow - -

Returns:

set of all codes in lookupWindow

getCodes

public static <T extends org.apache.uima.jcas.tcas.Annotation> Collection<String> getCodes(org.apache.uima.jcas.JCas jcas,
                                                                                           T lookupWindow,
                                                                                           String schemeName)

Parameters:

jcas - -

lookupWindow - -

schemeName - name of the scheme of interest

Returns:

set of ontology codes associated the named scheme

getCuis

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

Parameters:

annotations - -

Returns:

set of all Umls cuis associated with the annotations

getCuiCounts

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

Parameters:

annotations - -

Returns:

map of all Umls cuis associated with the annotations and the counts of those cuis

getTuis

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

Parameters:

annotations - -

Returns:

set of all Umls tuis associated with the annotation

getSchemeCodes

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

Parameters:

annotations - -

Returns:

map of ontology scheme names to a set of ontology codes associated each scheme

getCodes

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

Parameters:

annotations - -

Returns:

set of ontology codes associated with all schemes

getCodes

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

Parameters:

annotations - -

schemeName - name of the scheme of interest

Returns:

set of ontology codes associated the named scheme

getAnnotationsByCui

public static Collection<IdentifiedAnnotation> getAnnotationsByCui(org.apache.uima.jcas.JCas jcas,
                                                                   String cui)

Parameters:

jcas - -

cui - cui of interest

Returns:

all IdentifiedAnnotations that have the given cui

getAnnotationsByTui

public static Collection<IdentifiedAnnotation> getAnnotationsByTui(org.apache.uima.jcas.JCas jcas,
                                                                   String tui)

Parameters:

jcas - -

tui - tui of interest

Returns:

all IdentifiedAnnotations that have the given tui

getAnnotationsByCode

public static Collection<IdentifiedAnnotation> getAnnotationsByCode(org.apache.uima.jcas.JCas jcas,
                                                                    String code)

Parameters:

jcas - -

code - code of interest

Returns:

all IdentifiedAnnotations that have the given code

getAnnotationsByCui

public static <T extends org.apache.uima.jcas.tcas.Annotation> Collection<IdentifiedAnnotation> getAnnotationsByCui(org.apache.uima.jcas.JCas jcas,
                                                                                                                    T lookupWindow,
                                                                                                                    String cui)

Parameters:

jcas - -

lookupWindow - -

cui - cui of interest

Returns:

all IdentifiedAnnotations that have the given cui

getAnnotationsByTui

public static <T extends org.apache.uima.jcas.tcas.Annotation> Collection<IdentifiedAnnotation> getAnnotationsByTui(org.apache.uima.jcas.JCas jcas,
                                                                                                                    T lookupWindow,
                                                                                                                    String tui)

Parameters:

jcas - -

lookupWindow - -

tui - tui of interest

Returns:

all IdentifiedAnnotations that have the given tui

getAnnotationsByCode

public static <T extends org.apache.uima.jcas.tcas.Annotation> Collection<IdentifiedAnnotation> getAnnotationsByCode(org.apache.uima.jcas.JCas jcas,
                                                                                                                     T lookupWindow,
                                                                                                                     String code)

Parameters:

jcas - -

lookupWindow - -

code - code of interest

Returns:

all IdentifiedAnnotations that have the given code

getAnnotationsByCui

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

Parameters:

annotations - annotations for which codes should be found

cui - cui of interest

Returns:

all IdentifiedAnnotations that have the given cui

getAnnotationsByTui

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

Parameters:

annotations - annotations for which codes should be found

tui - tui of interest

Returns:

all IdentifiedAnnotations that have the given tui

getAnnotationsByCode

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

Parameters:

annotations - annotations for which codes should be found

code - code of interest

Returns:

all IdentifiedAnnotations that have the given code