EssentialAnnotationUtil

final public class EssentialAnnotationUtil

Utility to fetch integrated, coordinated collections of entities, events, and coreferences in a CAS.

• Author: SPF , chip-nlp
• Version: %I%
• Since: 12/29/2017
  
  

static private Collection<IdentifiedAnnotation> getEssentialAnnotations( final Collection<IdentifiedAnnotation> annotations )

From a collection of annotations, get the events, times, and entities.

• Parameters:
  • annotations all IdentifiedAnnotations, regardless of type.
• Returns: Collection of EventMentions, TimeMentions, and EntityMentions.
  
  

static private void cullToEssentialAnnotations( final Collection<Collection<IdentifiedAnnotation>> annotationCollections )

From multiple collections of annotations, remove everything that isn't an event, time, or entity.

• Parameters:
  • annotationCollections all IdentifiedAnnotations, regardless of type.
    
    

static private Collection<IdentifiedAnnotation> getNonEssentialAnnotations( final Collection<IdentifiedAnnotation> allAnnotations, final Collection<IdentifiedAnnotation> unwantedAnnotations )

From a collection of annotations, get everything that is not in the collection of essential annotations.

• Parameters:
  • allAnnotations all IdentifiedAnnotations, regardless of type.
  • unwantedAnnotations unwanted annotations.
• Returns: Collection of EventMentions, TimeMentions, and EntityMentions.
  
  

static public Collection<IdentifiedAnnotation> getRequiredAnnotations( final JCas jCas, final Map<IdentifiedAnnotation, Collection<Integer>> corefIndexed )

To allow fulfilled relations and coreference chains, we need essential annotations and related non-essential annotations.

• Parameters:
  • jCas ye olde ...
  • corefIndexed map of identified annotations to coreference chains containing them.
• Returns: all events, times, and entities, plus annotations that are required for coreferences and relations.
  
  

static public Collection<IdentifiedAnnotation> getRequiredAnnotations( final JCas jCas, final Collection<IdentifiedAnnotation> allAnnotations, final Map<IdentifiedAnnotation, Collection<Integer>> corefIndexed )

To allow fulfilled relations and coreference chains, we need essential annotations and related non-essential annotations.

• Parameters:
  • jCas ye olds ...
  • allAnnotations all IdentifiedAnnotations, regardless of type.
  • corefIndexed map of identified annotations to coreference chains containing them.
• Returns: all events, times, and entities, plus annotations that are required for coreferences and relations.
  
  

static public Collection<IdentifiedAnnotation> getRequiredAnnotations( final Collection<IdentifiedAnnotation> allAnnotations, final Map<IdentifiedAnnotation, Collection<Integer>> corefIndexed, final Collection<BinaryTextRelation> relations )

To allow fulfilled relations and coreference chains, we need essential annotations and related non-essential annotations.

• Parameters:
  • allAnnotations all IdentifiedAnnotations, regardless of type.
  • corefIndexed map of identified annotations to coreference chains containing them.
  • relations relations between annotations.
• Returns: all events, times, and entities, plus annotations that are required for coreferences and relations.
  
  

static public Map<IdentifiedAnnotation, Collection<Integer>> createMarkableCorefs( final JCas jCas )

• Parameters:
  • jCas ye olde ...
• Returns: a map of coreferent annotations to indexed chain numbers.
  
  

static public Map<IdentifiedAnnotation, Collection<Integer>> createMarkableCorefs( final Collection<CollectionTextRelation> corefs, final Map<Markable, IdentifiedAnnotation> markableAnnotations )

• Parameters:
  • corefs coreference chains.
  • markableAnnotations annotations that should be allowed in coreferences.
• Returns: a map of coreferent annotations to indexed chain numbers.
  
  

static public Map<IdentifiedAnnotation, Collection<Integer>> createMarkableAssertedCorefs( final Collection<CollectionTextRelation> corefs, final Map<Markable, IdentifiedAnnotation> markableAnnotations )

Sometimes there will be two overlapping annotations, 1 affirmed 1 negated. Use this for matching assertions in coreference chains.

• Parameters:
  • corefs coreference chains.
  • markableAnnotations annotations that should be allowed in coreferences.
• Returns: a map of annotations to indexed chain numbers, separated by assertion status.
  
  

static public Map<IdentifiedAnnotation, Collection<Integer>> createAllMarkableAssertedCorefs( final JCas jCas )

Sometimes there will be two overlapping annotations, 1 affirmed 1 negated. Use this for matching assertions in coreference chains.

• Parameters:
  • jCas ye olde ...
• Returns: a map of annotations to indexed chain numbers, separated by assertion status.
  
  

static public Map<IdentifiedAnnotation, Collection<Integer>> createAllMarkableAssertedCorefs( final Collection<CollectionTextRelation> corefs, final Map<Markable, Collection<IdentifiedAnnotation>> markableAnnotations )

Sometimes there will be two overlapping annotations, 1 affirmed 1 negated. Use this for matching assertions in coreference chains.

• Parameters:
  • corefs coreference chains.
  • markableAnnotations annotations that should be allowed in coreferences.
• Returns: a map of annotations to indexed chain numbers, separated by assertion status.
  
  

static private String getAssertion( final IdentifiedAnnotation annotation )

• Parameters:
  • annotation -
• Returns: string of concatenated assertion values: AFFIRMED, NEGATED, UNCERTAIN, GENERIC, CONDITIONAL.
  
  

static private Map<Markable, IdentifiedAnnotation> mapMarkableAnnotations( final JCas jCas, final Collection<CollectionTextRelation> corefs )

We can create a map of "best fit" single identified annotations for each coreference markable.

• Parameters:
  • jCas ye olde ...
  • corefs collection of coref relations.
• Returns: map of each coref markable to an identified annotation.
  
  

static public Map<Markable, Collection<IdentifiedAnnotation>> mapAllMarkableAnnotations( final JCas jCas, final Collection<CollectionTextRelation> corefs )

We can create a map of multiple overlapping identified annotations for each coreference markable.

• Parameters:
  • jCas ye olde ...
  • corefs collection of coref relations.
• Returns: map of each coref markable to an identified annotation.
  
  

static public ConllDependencyNode getNominalHeadNode( final List<ConllDependencyNode> nodes )

Finds the head node out of a few ConllDependencyNodes. Biased toward nouns.

• Parameters:

  • nodes dependency nodes.

• Returns: best head node.

static public Collection<IdentifiedAnnotation> getRelationAnnotations( final Collection<BinaryTextRelation> relations )

• Parameters:
  • relations -
• Returns: all annotations in relations.
  
  

static private Collection<IdentifiedAnnotation> getEventMentions( final Collection<IdentifiedAnnotation> annotations )

• Parameters:
  • annotations all IdentifiedAnnotations, regardless of type.
• Returns: collection of events in the annotations.
  
  

static private Map<IdentifiedAnnotation, Collection<IdentifiedAnnotation>> getAnnotationEvents( final Map<TextSpan, Collection<IdentifiedAnnotation>> annotationMap )

• Parameters:
  • annotationMap map of TextSpans for IdentifiedAnnotations with those text spans.
• Returns: map of annotations to events.
  
  

static private String createSectionName( final Segment section )

There may be multiple sections with the same preferred name. We want unique names for each section.

• Parameters:
  • section -
• Returns: Section Name + section ID or section ID or section Name or "Unknown Section".