Modifier and Type | Method and Description |
---|---|
List<org.cleartk.ml.Feature> |
GenericFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg) |
List<org.cleartk.ml.Feature> |
HistoryFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg) |
List<org.cleartk.ml.Feature> |
SubjectFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg) |
Modifier and Type | Method and Description |
---|---|
static Boolean |
GenericAttributeClassifier.getGeneric(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation mention) |
Modifier and Type | Method and Description |
---|---|
static Boolean |
HistoryAttributeClassifier.getHistory(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation mention) |
Modifier and Type | Method and Description |
---|---|
static String |
SubjectAttributeClassifier.getSubject(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation mention) |
Modifier and Type | Method and Description |
---|---|
void |
AssertionAnalysisEngine.debugAnnotationsInCas(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation annotation,
String label) |
static void |
AssertionAnalysisEngine.mapI2B2AssertionValueToCtakes(String assertionType,
IdentifiedAnnotation annotation) |
Modifier and Type | Method and Description |
---|---|
void |
ConceptConverterAnalysisEngine.processForEntityType(org.apache.uima.jcas.JCas jcas,
int annotationType,
Class<? extends IdentifiedAnnotation> annotationClass) |
Modifier and Type | Field and Description |
---|---|
protected List<org.cleartk.ml.feature.extractor.CleartkExtractor<IdentifiedAnnotation,BaseToken>> |
AssertionCleartkAnalysisEngine.contextFeatureExtractors |
protected org.cleartk.ml.feature.extractor.CleartkExtractor<IdentifiedAnnotation,BaseToken> |
AssertionCleartkAnalysisEngine.cuePhraseInWindowExtractor |
protected List<org.cleartk.ml.feature.extractor.FeatureExtractor1<IdentifiedAnnotation>> |
AssertionCleartkAnalysisEngine.entityFeatureExtractors |
protected List<org.cleartk.ml.feature.extractor.FeatureExtractor1<IdentifiedAnnotation>> |
AssertionCleartkAnalysisEngine.entityTreeExtractors |
protected List<org.cleartk.ml.feature.function.FeatureFunctionExtractor<IdentifiedAnnotation>> |
AssertionCleartkAnalysisEngine.featureFunctionExtractors |
protected List<org.cleartk.ml.feature.extractor.CleartkExtractor<IdentifiedAnnotation,BaseToken>> |
AssertionCleartkAnalysisEngine.tokenCleartkExtractors |
protected List<org.cleartk.ml.feature.extractor.CleartkExtractor<IdentifiedAnnotation,BaseToken>> |
AssertionCleartkAnalysisEngine.tokenContextFeatureExtractors |
Modifier and Type | Method and Description |
---|---|
abstract void |
AssertionCleartkAnalysisEngine.setClassLabel(IdentifiedAnnotation entityMention,
org.cleartk.ml.Instance<String> instance) |
void |
ConditionalCleartkAnalysisEngine.setClassLabel(IdentifiedAnnotation entityOrEventMention,
org.cleartk.ml.Instance<String> instance) |
void |
GenericCleartkAnalysisEngine.setClassLabel(IdentifiedAnnotation entityOrEventMention,
org.cleartk.ml.Instance<String> instance) |
void |
HistoryCleartkAnalysisEngine.setClassLabel(IdentifiedAnnotation entityOrEventMention,
org.cleartk.ml.Instance<String> instance) |
void |
PolarityCleartkAnalysisEngine.setClassLabel(IdentifiedAnnotation entityOrEventMention,
org.cleartk.ml.Instance<String> instance) |
void |
PolarityFedaCleartkAnalysisEngine.setClassLabel(IdentifiedAnnotation entityOrEventMention,
org.cleartk.ml.Instance<String> instance) |
void |
SubjectCleartkAnalysisEngine.setClassLabel(IdentifiedAnnotation entityOrEventMention,
org.cleartk.ml.Instance<String> instance) |
void |
UncertaintyCleartkAnalysisEngine.setClassLabel(IdentifiedAnnotation entityOrEventMention,
org.cleartk.ml.Instance<String> instance) |
Modifier and Type | Method and Description |
---|---|
List<org.cleartk.ml.Feature> |
AboveLeftFragmentExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation annotation) |
List<org.cleartk.ml.Feature> |
AboveRightFragmentExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation annotation) |
List<org.cleartk.ml.Feature> |
AssertionAboveLeftTreeExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation annotation) |
List<org.cleartk.ml.Feature> |
AssertionDependencyTreeExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1) |
List<org.cleartk.ml.Feature> |
ContextWordWindowExtractor.extract(org.apache.uima.jcas.JCas view,
IdentifiedAnnotation mention) |
List<org.cleartk.ml.Feature> |
DependencyPathRegexpFeatureExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation mention) |
List<org.cleartk.ml.Feature> |
DependencyWordsFragmentExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation mention) |
List<org.cleartk.ml.Feature> |
NegationDependencyFeatureExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation focusAnnotation) |
abstract List<org.cleartk.ml.Feature> |
TreeFragmentFeatureExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation annotation) |
List<org.cleartk.ml.Feature> |
UncertaintyFeatureExtractor.extract(org.apache.uima.jcas.JCas view,
IdentifiedAnnotation focusAnnotation) |
static ArrayList<String> |
SRLFeatureExtractor.getEntityFeats(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation ent,
Sentence sent) |
Modifier and Type | Method and Description |
---|---|
static SimpleTree |
GenerateTreeRepresentation.getNegationTree(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation mention,
SemanticClasses sems) |
static SimpleTree |
GenerateTreeRepresentation.getUncertaintyTree(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation mention,
SemanticClasses sems) |
Modifier and Type | Method and Description |
---|---|
protected String |
BagOfCUIsGenerator.extractInformation(IdentifiedAnnotation t) |
Modifier and Type | Method and Description |
---|---|
protected String |
JdbcWriterTemplate.createBlob(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation annotation)
I2b2 wants annotation begin and end offsets plus the covered text
|
Modifier and Type | Method and Description |
---|---|
protected void |
JdbcWriterTemplate.saveAnnotations(org.apache.uima.jcas.JCas jcas,
Map<JdbcWriterTemplate.I2b2FieldInfo,Object> fieldInfoValues,
String cui,
String preferredText,
Iterable<IdentifiedAnnotation> annotations,
boolean saveAffirmed) |
Modifier and Type | Method and Description |
---|---|
static Collection<IdentifiedAnnotation> |
OntologyConceptUtil.getAnnotationsByCode(Collection<IdentifiedAnnotation> annotations,
String code) |
static Collection<IdentifiedAnnotation> |
OntologyConceptUtil.getAnnotationsByCode(org.apache.uima.jcas.JCas jcas,
String code) |
static <T extends org.apache.uima.jcas.tcas.Annotation> |
OntologyConceptUtil.getAnnotationsByCode(org.apache.uima.jcas.JCas jcas,
T lookupWindow,
String code) |
static Collection<IdentifiedAnnotation> |
OntologyConceptUtil.getAnnotationsByCui(Collection<IdentifiedAnnotation> annotations,
String cui) |
static Collection<IdentifiedAnnotation> |
OntologyConceptUtil.getAnnotationsByCui(org.apache.uima.jcas.JCas jcas,
String cui) |
static <T extends org.apache.uima.jcas.tcas.Annotation> |
OntologyConceptUtil.getAnnotationsByCui(org.apache.uima.jcas.JCas jcas,
T lookupWindow,
String cui) |
static Collection<IdentifiedAnnotation> |
OntologyConceptUtil.getAnnotationsByTui(Collection<IdentifiedAnnotation> annotations,
String tui) |
static Collection<IdentifiedAnnotation> |
OntologyConceptUtil.getAnnotationsByTui(org.apache.uima.jcas.JCas jcas,
String tui) |
static <T extends org.apache.uima.jcas.tcas.Annotation> |
OntologyConceptUtil.getAnnotationsByTui(org.apache.uima.jcas.JCas jcas,
T lookupWindow,
String tui) |
Modifier and Type | Field and Description |
---|---|
protected HashSet<IdentifiedAnnotation> |
EventCoreferenceAnnotator.foundAnaphors |
Modifier and Type | Method and Description |
---|---|
IdentifiedAnnotation |
MentionClusterCoreferenceAnnotator.CollectionTextRelationIdentifiedAnnotationPair.getMention() |
IdentifiedAnnotation |
MentionClusterRankingCoreferenceAnnotator.CollectionTextRelationIdentifiedAnnotationPair.getMention() |
Modifier and Type | Method and Description |
---|---|
protected List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>> |
EventCoreferenceAnnotator.getFeatureExtractors() |
protected List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>> |
EventCoreferenceAnnotator.getFeatureExtractors() |
protected List<RelationFeaturesExtractor<CollectionTextRelation,IdentifiedAnnotation>> |
MentionClusterCoreferenceAnnotator.getFeatureExtractors() |
protected List<RelationFeaturesExtractor<CollectionTextRelation,IdentifiedAnnotation>> |
MentionClusterRankingCoreferenceAnnotator.getFeatureExtractors() |
Modifier and Type | Method and Description |
---|---|
protected void |
MentionClusterRankingCoreferenceAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
CollectionTextRelation cluster,
IdentifiedAnnotation mention,
String predictedCategory)
Create a UIMA relation type based on arguments and the relation label.
|
protected void |
MentionClusterCoreferenceAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
CollectionTextRelation cluster,
IdentifiedAnnotation mention,
String predictedCategory,
Double confidence)
Create a UIMA relation type based on arguments and the relation label.
|
protected void |
EventCoreferenceAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation ante,
IdentifiedAnnotation ana,
String predictedCategory) |
protected Iterable<MentionClusterRankingCoreferenceAnnotator.CollectionTextRelationIdentifiedAnnotationPair> |
MentionClusterRankingCoreferenceAnnotator.getCandidateRelationArgumentPairs(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation mention) |
protected List<MentionClusterRankingCoreferenceAnnotator.CollectionTextRelationIdentifiedAnnotationPair> |
MentionClusterRankingCoreferenceAnnotator.getHeadwordMatchPairs(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation mention,
int sentDist) |
protected String |
EventCoreferenceAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation ante,
IdentifiedAnnotation ana) |
protected String |
MentionClusterCoreferenceAnnotator.getRelationCategory(Map<MentionClusterCoreferenceAnnotator.CollectionTextRelationIdentifiedAnnotationPair,CollectionTextRelationIdentifiedAnnotationRelation> relationLookup,
CollectionTextRelation cluster,
IdentifiedAnnotation mention)
Looks up the arguments in the specified lookup table and converts the
relation into a label for classification
|
protected String |
MentionClusterRankingCoreferenceAnnotator.getRelationCategory(Map<MentionClusterRankingCoreferenceAnnotator.CollectionTextRelationIdentifiedAnnotationPair,CollectionTextRelationIdentifiedAnnotationRelation> relationLookup,
CollectionTextRelation cluster,
IdentifiedAnnotation mention)
Looks up the arguments in the specified lookup table and converts the
relation into a label for classification
|
protected List<MentionClusterRankingCoreferenceAnnotator.CollectionTextRelationIdentifiedAnnotationPair> |
MentionClusterRankingCoreferenceAnnotator.getSectionHeaderPairs(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation mention,
int sentDist) |
protected List<MentionClusterRankingCoreferenceAnnotator.CollectionTextRelationIdentifiedAnnotationPair> |
MentionClusterRankingCoreferenceAnnotator.getSentenceDistancePairs(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation mention,
int sentDist) |
static int |
EventCoreferenceAnnotator.sentDist(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
static int |
EventCoreferenceAnnotator.sentsBetween(IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
Constructor and Description |
---|
CollectionTextRelationIdentifiedAnnotationPair(CollectionTextRelation cluster,
IdentifiedAnnotation mention) |
CollectionTextRelationIdentifiedAnnotationPair(CollectionTextRelation cluster,
IdentifiedAnnotation mention) |
Modifier and Type | Method and Description |
---|---|
static boolean |
UMLSFeatureExtractor.alias(IdentifiedAnnotation a1,
IdentifiedAnnotation a2) |
List<org.cleartk.ml.Feature> |
AttributeFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation ante,
IdentifiedAnnotation ana) |
List<org.cleartk.ml.Feature> |
CorefSyntaxFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
DistanceFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
DistSemFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
SalienceFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation ante,
IdentifiedAnnotation ana) |
List<org.cleartk.ml.Feature> |
SectionFeatureExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation ante,
IdentifiedAnnotation ana) |
List<org.cleartk.ml.Feature> |
StringMatchingFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
TemporalFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
TokenFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
UMLSFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
static boolean |
TokenFeatureExtractor.isGeneric(IdentifiedAnnotation mention) |
static boolean |
TokenFeatureExtractor.isHistory(IdentifiedAnnotation mention) |
static boolean |
TokenFeatureExtractor.isNegated(IdentifiedAnnotation mention) |
static boolean |
TokenFeatureExtractor.isPatient(IdentifiedAnnotation mention) |
static boolean |
StringMatchingFeatureExtractor.isPronoun(IdentifiedAnnotation a1) |
static boolean |
TokenFeatureExtractor.isUncertain(IdentifiedAnnotation mention) |
Modifier and Type | Method and Description |
---|---|
List<org.cleartk.ml.Feature> |
MentionClusterAgreementFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
CollectionTextRelation cluster,
IdentifiedAnnotation mention) |
List<org.cleartk.ml.Feature> |
MentionClusterAttributeFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
CollectionTextRelation cluster,
IdentifiedAnnotation mention) |
List<org.cleartk.ml.Feature> |
MentionClusterAttributeVectorExtractor.extract(org.apache.uima.jcas.JCas jCas,
CollectionTextRelation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
MentionClusterDepHeadExtractor.extract(org.apache.uima.jcas.JCas jCas,
CollectionTextRelation cluster,
IdentifiedAnnotation mention) |
List<org.cleartk.ml.Feature> |
MentionClusterDistanceFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
CollectionTextRelation cluster,
IdentifiedAnnotation mention) |
List<org.cleartk.ml.Feature> |
MentionClusterDistSemExtractor.extract(org.apache.uima.jcas.JCas jCas,
CollectionTextRelation cluster,
IdentifiedAnnotation mention) |
List<org.cleartk.ml.Feature> |
MentionClusterSalienceFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
CollectionTextRelation cluster,
IdentifiedAnnotation mention) |
List<org.cleartk.ml.Feature> |
MentionClusterSectionFeaturesExtractor.extract(org.apache.uima.jcas.JCas jcas,
CollectionTextRelation cluster,
IdentifiedAnnotation mention) |
List<org.cleartk.ml.Feature> |
MentionClusterSemTypeDepPrefsFeatureExtractor.extract(org.apache.uima.jcas.JCas jcas,
CollectionTextRelation cluster,
IdentifiedAnnotation mention) |
List<org.cleartk.ml.Feature> |
MentionClusterStackFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
CollectionTextRelation cluster,
IdentifiedAnnotation mention) |
List<org.cleartk.ml.Feature> |
MentionClusterStringFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
CollectionTextRelation cluster,
IdentifiedAnnotation mention) |
List<org.cleartk.ml.Feature> |
MentionClusterUMLSFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
CollectionTextRelation cluster,
IdentifiedAnnotation mention) |
Modifier and Type | Method and Description |
---|---|
static Map<Markable,List<IdentifiedAnnotation>> |
MarkableUtilities.indexCoveringUmlsAnnotations(org.apache.uima.jcas.JCas jCas) |
Modifier and Type | Method and Description |
---|---|
IdentifiedAnnotation |
RelationExtractorAnnotator.IdentifiedAnnotationPair.getArg1() |
IdentifiedAnnotation |
RelationExtractorAnnotator.IdentifiedAnnotationPair.getArg2() |
Modifier and Type | Method and Description |
---|---|
protected List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>> |
RelationExtractorAnnotator.getFeatureExtractors()
Defines the list of feature extractors used by the classifier.
|
protected List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>> |
RelationExtractorAnnotator.getFeatureExtractors()
Defines the list of feature extractors used by the classifier.
|
Modifier and Type | Method and Description |
---|---|
protected void |
CausesBringsAboutRelationExtractorAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory) |
protected void |
DegreeOfRelationExtractorAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory) |
protected void |
LocationOfRelationExtractorAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory) |
protected void |
ManagesTreatsRelationExtractorAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory) |
protected void |
ManifestationOfRelationExtractorAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory) |
protected void |
RelationExtractorAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory)
Create a UIMA relation type based on arguments and the relation label.
|
static List<Integer> |
IdentifiedAnnotationExpander.expandToNP(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation identifiedAnnotation) |
static String |
IdentifiedAnnotationExpander.getEnclosingNP(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation identifiedAnnotation) |
protected String |
RelationExtractorAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
Looks up the arguments in the specified lookup table and converts the
relation into a label for classification
|
Constructor and Description |
---|
IdentifiedAnnotationPair(IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
Modifier and Type | Method and Description |
---|---|
List<org.cleartk.ml.Feature> |
ArgumentOrderFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
DependencyPathFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
DependencyTreeFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
EmbeddingFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
EntitySpanFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
FlatTreeFeatureExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
NamedEntityFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
PartOfSpeechFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
PETFeatureExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
PhraseChunkingExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
PrepositionFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
PunctuationFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
TokenFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation mention1,
IdentifiedAnnotation mention2) |
List<org.cleartk.ml.Feature> |
TreeFragmentFeatureExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
static List<org.cleartk.ml.Feature> |
WordNetFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation identifiedAnnotation,
edu.mit.jwi.IDictionary iDictionary) |
static List<org.cleartk.ml.Feature> |
DependencyTreeFeaturesExtractor.extractForNode(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation mention,
String ftrPrefix) |
Modifier and Type | Method and Description |
---|---|
static int |
GoldAnnotationStatsCalculator.getTokenDistance(org.apache.uima.jcas.JCas systemView,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
Modifier and Type | Method and Description |
---|---|
static HashSet<String> |
SelectiveRelationAnnotationViewer.getOntologyConceptCodes(IdentifiedAnnotation identifiedAnnotation)
Get the CUIs, RxNorm codes specified for this entity.
|
Modifier and Type | Method and Description |
---|---|
IdentifiedAnnotation |
SideEffectAnnotation.getDrug()
getter for drug - gets
|
IdentifiedAnnotation |
SideEffectAnnotation.getSideEffect()
getter for sideEffect - gets side effect mention in NamedEntity
|
Modifier and Type | Method and Description |
---|---|
void |
SideEffectAnnotation.setDrug(IdentifiedAnnotation v)
setter for drug - sets
|
void |
SideEffectAnnotation.setSideEffect(IdentifiedAnnotation v)
setter for sideEffect - sets side effect mention in NamedEntity
|
Modifier and Type | Method and Description |
---|---|
static boolean |
SEUtil.isInUpperCaseStringLine(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation nea)
Return true if the given NE belongs to the line consisting of a upper-cased string without " - "
|
Modifier and Type | Class and Description |
---|---|
class |
NonSmokerNamedEntityAnnotation
Updated by JCasGen Mon Apr 24 21:42:45 EDT 2017
XML source: /private/tmp/murali/ctakes/ctakes-4.0.0/ctakes-smoking-status/target/jcasgen/typesystem.xml
|
class |
SmokerNamedEntityAnnotation
Updated by JCasGen Mon Apr 24 21:42:45 EDT 2017
XML source: /private/tmp/murali/ctakes/ctakes-4.0.0/ctakes-smoking-status/target/jcasgen/typesystem.xml
|
class |
UnknownSmokerNamedEntityAnnotation
Updated by JCasGen Mon Apr 24 21:42:45 EDT 2017
XML source: /private/tmp/murali/ctakes/ctakes-4.0.0/ctakes-smoking-status/target/jcasgen/typesystem.xml
|
Modifier and Type | Method and Description |
---|---|
IdentifiedAnnotation |
TemporalRelationExtractorAnnotator.IdentifiedAnnotationPair.getArg1() |
IdentifiedAnnotation |
TemporalRelationExtractorAnnotator.IdentifiedAnnotationPair.getArg2() |
Modifier and Type | Method and Description |
---|---|
protected void |
ConsecutiveSentencesEventEventRelationAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory) |
protected void |
ConsecutiveSentencesEventTimeRelationAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory) |
protected void |
EventEventCRFRelationAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory) |
protected void |
EventEventI2B2RelationAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory) |
protected void |
EventEventRelationGoldContainerAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory) |
protected void |
EventEventRelationSeedBasedAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory) |
protected void |
EventTimeI2B2RelationAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory) |
protected void |
EventTimeRelationAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory) |
protected void |
CrossSentenceTemporalRelationAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected void |
EventEventCNNAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence)
Dima's way of getting lables
|
protected void |
EventEventRelationAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected void |
EventTimeCNNAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected void |
EventTimeSelfRelationAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected void |
NeuralEventTimeSelfRelationAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected void |
TemporalRelationExtractorAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence)
Create a UIMA relation type based on arguments and the relation label.
|
protected void |
WithinSentenceBeforeRelationAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected String |
ConsecutiveSentencesEventEventRelationAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
ConsecutiveSentencesEventTimeRelationAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
EventEventCNNAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
original way of getting label
|
protected String |
EventEventCRFRelationAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
EventEventI2B2RelationAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
EventEventRelationAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
EventEventRelationGoldContainerAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
EventEventRelationSeedBasedAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
EventTimeCNNAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
Dima's way of getting lables
|
protected String |
EventTimeI2B2RelationAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
EventTimeRelationAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
EventTimeSelfRelationAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
NeuralEventTimeSelfRelationAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
TemporalRelationExtractorAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
Looks up the arguments in the specified lookup table and converts the
relation into a label for classification
|
Constructor and Description |
---|
IdentifiedAnnotationPair(IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
Modifier and Type | Method and Description |
---|---|
protected List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>> |
TreeHeightBaseline.getFeatureExtractors() |
protected List<RelationFeaturesExtractor<IdentifiedAnnotation,IdentifiedAnnotation>> |
TreeHeightBaseline.getFeatureExtractors() |
Modifier and Type | Method and Description |
---|---|
static void |
TemporalPETFlatExtractor.addOtherTimes(org.apache.uima.jcas.JCas jcas,
TopTreebankNode root,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
CheckSpecialWordRelationExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
ConjunctionRelationFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
CoordinateFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
DependencyFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
DependencyPathFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
DependingVerbsFeatureExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
DeterminerRelationFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
DocTimeRelFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
EmptyFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
EventArgumentPropertyExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
EventPositionRelationFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
EventTimeRelationFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
EventTimeRelationsFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
ListFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
MultiTokenFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation mention1,
IdentifiedAnnotation mention2) |
List<org.cleartk.ml.Feature> |
NearbyVerbTenseRelationExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
NearestFlagFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
NoOtherETPuntInBetweenFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation mention1,
IdentifiedAnnotation mention2) |
List<org.cleartk.ml.Feature> |
NumberOfEventsInTheSameSentenceExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
NumberOfEventTimeBetweenCandidatesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
OverlappedHeadFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation mention1,
IdentifiedAnnotation mention2)
Extract features for the pair of named entity mentions.
|
List<org.cleartk.ml.Feature> |
ParseFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
RelationEmbeddingFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
RelationSyntacticEmbeddingFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
RelationSyntacticETEmbeddingFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
SectionHeaderRelationExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
SpecialAnnotationRelationExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
SRLRelationFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
SyntacticParentFeatureExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
TemporalAttributeFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
TemporalAttributeForMixEventTimeExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
TemporalPETFlatExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
TimeXPropertyRelationFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
TimeXRelationFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
TokenPropertyFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
UMLSBasedTokenFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation mention1,
IdentifiedAnnotation mention2) |
List<org.cleartk.ml.Feature> |
UmlsFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
UnexpandedTokenFeaturesExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation mention1,
IdentifiedAnnotation mention2) |
Modifier and Type | Method and Description |
---|---|
List<org.cleartk.ml.Feature> |
DurationEventEventFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
DurationEventTimeFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
DurationTimeUnitFeatureExtractor.extract(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
Modifier and Type | Method and Description |
---|---|
static void |
TemporalPETExtractor.addOtherTimes(org.apache.uima.jcas.JCas jcas,
TopTreebankNode root,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
EventTimeFlatTreeFeatureExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
TemporalFTExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
TemporalPathExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
List<org.cleartk.ml.Feature> |
TemporalPETExtractor.extract(org.apache.uima.jcas.JCas jcas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
Modifier and Type | Method and Description |
---|---|
static String |
EventPrinterPipeline.expandToNP(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation identifiedAnnotation) |
Modifier and Type | Method and Description |
---|---|
protected void |
EventEventPosBasedAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected void |
EventEventPositionBasedAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected void |
EventEventTokenAndBIOBasedAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected void |
EventEventTokenAndPosBasedAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected void |
EventEventTokenBasedAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected void |
EventTimePosBasedAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected void |
EventTimePositionBasedAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected void |
EventTimeTokenAndBIOBasedAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected void |
EventTimeTokenAndPosBasedAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected void |
EventTimeTokenBasedAnnotator.createRelation(org.apache.uima.jcas.JCas jCas,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2,
String predictedCategory,
double confidence) |
protected String |
EventEventPosBasedAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
original way of getting label
|
protected String |
EventEventPositionBasedAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
original way of getting label
|
protected String |
EventEventTokenAndBIOBasedAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
original way of getting label
|
protected String |
EventEventTokenAndPosBasedAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
original way of getting label
|
protected String |
EventEventTokenBasedAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
original way of getting label
|
protected String |
EventTimePosBasedAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
Dima's way of getting lables
|
protected String |
EventTimePositionBasedAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
Dima's way of getting lables
|
protected String |
EventTimeTokenAndBIOBasedAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
Dima's way of getting lables
|
protected String |
EventTimeTokenAndPosBasedAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
Dima's way of getting lables
|
protected String |
EventTimeTokenBasedAnnotator.getRelationCategory(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2)
Dima's way of getting lables
|
protected String |
EventEventPosBasedAnnotator.getRelationCategory2(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
EventEventPositionBasedAnnotator.getRelationCategory2(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
EventEventTokenAndBIOBasedAnnotator.getRelationCategory2(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
EventEventTokenAndPosBasedAnnotator.getRelationCategory2(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
protected String |
EventEventTokenBasedAnnotator.getRelationCategory2(Map<List<org.apache.uima.jcas.tcas.Annotation>,BinaryTextRelation> relationLookup,
IdentifiedAnnotation arg1,
IdentifiedAnnotation arg2) |
static String |
EventEventTokenBasedAnnotator.getTokenTimexContext(org.apache.uima.jcas.JCas jCas,
Sentence sentence,
IdentifiedAnnotation arg1,
String leftType,
IdentifiedAnnotation arg2,
String rightType,
int contextSize) |
static String |
EventTimeTokenBasedAnnotator.getTokenTimexContext(org.apache.uima.jcas.JCas jCas,
Sentence sentence,
IdentifiedAnnotation arg1,
String leftType,
IdentifiedAnnotation arg2,
String rightType,
int contextSize) |
Modifier and Type | Method and Description |
---|---|
static String |
ArgContextProvider.getBIOContext(org.apache.uima.jcas.JCas jCas,
Sentence sentence,
IdentifiedAnnotation arg1,
String leftType,
IdentifiedAnnotation arg2,
String rightType,
int contextSize) |
static String |
ArgContextProvider.getEventEventPositionContext(org.apache.uima.jcas.JCas jCas,
Sentence sent,
IdentifiedAnnotation event1,
IdentifiedAnnotation event2)
Position features for event-event relations
|
static String |
ArgContextProvider.getEventTimePositionContext(org.apache.uima.jcas.JCas jCas,
Sentence sent,
IdentifiedAnnotation time,
IdentifiedAnnotation event)
Position features for event-time relations
|
Modifier and Type | Method and Description |
---|---|
IdentifiedAnnotation |
Element.getMentions(int i)
indexed getter for mentions - gets an indexed value -
|
Modifier and Type | Method and Description |
---|---|
void |
Element.setMentions(int i,
IdentifiedAnnotation v)
indexed setter for mentions - sets an indexed value -
|
Modifier and Type | Method and Description |
---|---|
IdentifiedAnnotation |
CollectionTextRelationIdentifiedAnnotationRelation.getMention()
getter for mention - gets
|
Modifier and Type | Method and Description |
---|---|
void |
CollectionTextRelationIdentifiedAnnotationRelation.setMention(IdentifiedAnnotation v)
setter for mention - sets
|
Modifier and Type | Class and Description |
---|---|
class |
BodyLateralityModifier
The proximity of the location in anatomical terms (distal, proximal, superior, anterior and etc.).
|
class |
BodySideModifier
Value set: unmarked (default), left, right, bilateral
Updated by JCasGen Mon Apr 24 21:42:44 EDT 2017
XML source: /private/tmp/murali/ctakes/ctakes-4.0.0/ctakes-side-effect/target/jcasgen/typesystem.xml
|
class |
ConditionalModifier
The Conditional modifier refers to mentions which could exist under certain circumstances.
|
class |
ContextAnnotation
Contextual information of an entity.
|
class |
CourseModifier
An indication of progress or decline of a condition.
|
class |
DateAnnotation
Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.DateAnnotation
Updated by JCasGen Mon Apr 24 21:42:44 EDT 2017
XML source: /private/tmp/murali/ctakes/ctakes-4.0.0/ctakes-side-effect/target/jcasgen/typesystem.xml
|
class |
EntityMention
A text string (IdentifiedAnnotation) that refers to an Entity.
|
class |
EventMention
A text string (IdentifiedAnnotation) that refers to an Event.
|
class |
FractionAnnotation
Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.FractionAnnotation
Updated by JCasGen Mon Apr 24 21:42:44 EDT 2017
XML source: /private/tmp/murali/ctakes/ctakes-4.0.0/ctakes-side-effect/target/jcasgen/typesystem.xml
|
class |
GenericModifier
The Generic modifier indicates that a named entity mention is generic, i.e., not related to the instance of a disorder, sign/symptom, etc.
|
class |
HistoryOfModifier
An indication of explicit mentioning of a past history.
|
class |
LabDeltaFlagModifier
An indicator to warn that the laboratory test result has changed significantly from the previous identical laboratory test result.
|
class |
LabEstimatedModifier
Signals that the lab value was estimated, e.g., "GFR (estimated): 81".
|
class |
LabInterpretationModifier
Test result interpretations organized in a valued list e.g., "rare cells seen" or "few cells seen" in urinalysis, now combined with very_abnormal and abnormal.
|
class |
LabReferenceRangeModifier
Holds a narrative (i.e.
|
class |
LabValueModifier
Quantitative results of a laboratory, with number and unit.
|
class |
Markable
A type for representing text spans that can potentially be linked together via coreference.
|
class |
MeasurementAnnotation
Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.MeasurementAnnotation
Updated by JCasGen Mon Apr 24 21:42:44 EDT 2017
XML source: /private/tmp/murali/ctakes/ctakes-4.0.0/ctakes-side-effect/target/jcasgen/typesystem.xml
|
class |
MedicationAllergyModifier
Indication of whether the medication is mentioned in the context of Allergies.
|
class |
MedicationDosageModifier
Dosage indicates how much of a prescribed drug should be taken.
|
class |
MedicationDurationModifier
The amount of time after which a medication should stop being used, e.g., "2 weeks" in "one 5 mg tablet twice-a-day for 2 weeks"
Updated by JCasGen Mon Apr 24 21:42:44 EDT 2017
XML source: /private/tmp/murali/ctakes/ctakes-4.0.0/ctakes-side-effect/target/jcasgen/typesystem.xml
|
class |
MedicationFormModifier
Form of this medication.
|
class |
MedicationFrequencyModifier
How often a medication should be used.
|
class |
MedicationRouteModifier
Means by which the medication was taken or administered.
|
class |
MedicationStatusChangeModifier
Status refers to the whether the medication is currently being taken or not.
|
class |
MedicationStrengthModifier
Strength indicates the strength number and unit of the prescribed drug.
|
class |
Modifier
A text string (IdentifiedAnnotation) that refers to an Attribute.
|
class |
PersonTitleAnnotation
Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.PersonTitleAnnotation
Updated by JCasGen Mon Apr 24 21:42:44 EDT 2017
XML source: /private/tmp/murali/ctakes/ctakes-4.0.0/ctakes-side-effect/target/jcasgen/typesystem.xml
|
class |
PolarityModifier
Used to indicate that a procedure or assertion did not occur or does not exist.
|
class |
ProcedureDeviceModifier
Corresponds to the UMLS Devices semantic group: medical device and research device.
|
class |
ProcedureMethodModifier
The way or the equipment used to give or administration something (medication, test).
|
class |
RangeAnnotation
Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.RangeAnnotation
Updated by JCasGen Mon Apr 24 21:42:44 EDT 2017
XML source: /private/tmp/murali/ctakes/ctakes-4.0.0/ctakes-side-effect/target/jcasgen/typesystem.xml
|
class |
RomanNumeralAnnotation
Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.RomanNumeralAnnotation
Updated by JCasGen Mon Apr 24 21:42:44 EDT 2017
XML source: /private/tmp/murali/ctakes/ctakes-4.0.0/ctakes-side-effect/target/jcasgen/typesystem.xml
|
class |
SeverityModifier
An explicitly-mentioned indication of the seriousness of a condition.
|
class |
SubjectModifier
The person the observation is on, i.e., a Person mention.
|
class |
TimeAnnotation
Equivalent to cTAKES: edu.mayo.bmi.uima.cdt.type.TimeAnnotation
Updated by JCasGen Mon Apr 24 21:42:44 EDT 2017
XML source: /private/tmp/murali/ctakes/ctakes-4.0.0/ctakes-side-effect/target/jcasgen/typesystem.xml
|
class |
TimeMention
A text string (IdentifiedAnnotation) that refers to a Time (i.e., TIMEX3).
|
class |
UncertaintyModifier
An introduction of a measure of doubt into a statement.
|
Modifier and Type | Method and Description |
---|---|
protected void |
SenseDisambiguatorAnnotator.disambiguate(org.apache.uima.jcas.JCas jcas,
List<IdentifiedAnnotation> listNE) |
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