de.julielab.jcore.ae.jnet.uima

Class EntityAnnotator

java.lang.Object

org.apache.uima.analysis_component.AnalysisComponent_ImplBase

org.apache.uima.analysis_component.Annotator_ImplBase

org.apache.uima.analysis_component.JCasAnnotator_ImplBase

de.julielab.jcore.ae.jnet.uima.EntityAnnotator

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent

public class EntityAnnotator
extends org.apache.uima.analysis_component.JCasAnnotator_ImplBase

Field Summary

Fields

Modifier and Type	Field and Description
protected static String	ABBREV_PATTERN
Pattern	abbrevPattern
protected float	confidenceThresholdForConsistencyPreservation
protected ConsistencyPreservation	consistencyPreservation
protected TreeSet<String>	entityMentionTypes
protected boolean	expandAbbr
protected NegativeList	negativeList
protected boolean	showSegmentConf

Constructor Summary

Constructors

Constructor and Description
EntityAnnotator()

Method Summary

Modifier and Type	Method and Description
protected Sentence	createUnitSentence(List<Token> tokenList, org.apache.uima.jcas.JCas JCas, ArrayList<HashMap<String,String>> metaList, JCoReCoverIndex<Abbreviation> abbreviationIndex, JCoReCoverIndex<Token> tokenIndex) Takes all info about meta data and generates the corresponding unit sequence represented by a Sentence object.
protected boolean	ignoreLabel(org.apache.uima.jcas.JCas aJCas, int start, int end, JCoReCoverIndex<Abbreviation> abbreviationIndex) tests whether annotation should be ignored as this label is on a not introduced abbreviation
void	initialize(org.apache.uima.UimaContext aContext) Initialisiation of UIMA-JNET.
void	process(org.apache.uima.jcas.JCas aJCas) process current CAS.
protected Sentence	removeDuplicatedTokens(Sentence unitSentence) removes duplicate tokens in a unit sentence (i.e., tokens having the same offset position).
void	writeToCAS(Sentence unitSentence, org.apache.uima.jcas.JCas aJCas, JCoReCoverIndex<Abbreviation> abbreviationIndex) creates the respective uima annotations from JNET's predictions.

Methods inherited from class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

getRequiredCasInterface, process

Methods inherited from class org.apache.uima.analysis_component.Annotator_ImplBase

getCasInstancesRequired, hasNext, next

Methods inherited from class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

batchProcessComplete, collectionProcessComplete, destroy, getContext, getResultSpecification, reconfigure, setResultSpecification

Methods inherited from class java.lang.Object

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

Field Detail

ABBREV_PATTERN

protected static final String ABBREV_PATTERN

See Also:

Constant Field Values

abbrevPattern

public Pattern abbrevPattern

expandAbbr

protected boolean expandAbbr

consistencyPreservation

protected ConsistencyPreservation consistencyPreservation

confidenceThresholdForConsistencyPreservation

protected float confidenceThresholdForConsistencyPreservation

showSegmentConf

protected boolean showSegmentConf

entityMentionTypes

protected TreeSet<String> entityMentionTypes

negativeList

protected NegativeList negativeList

Constructor Detail

EntityAnnotator

public EntityAnnotator()

Method Detail

initialize

public void initialize(org.apache.uima.UimaContext aContext)
                throws org.apache.uima.resource.ResourceInitializationException

Initialisiation of UIMA-JNET. Reads in and checks descriptor's parameters.

Specified by:

initialize in interface org.apache.uima.analysis_component.AnalysisComponent

Overrides:

initialize in class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

Throws:

org.apache.uima.resource.ResourceInitializationException

process

public void process(org.apache.uima.jcas.JCas aJCas)
             throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

process current CAS. In case, abbreviation expansion is turned on, the abbreviation is replaced by its full form which is used during prediction. The labels of this full form are then applied to the original, short form.

Specified by:

process in class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

removeDuplicatedTokens

protected Sentence removeDuplicatedTokens(Sentence unitSentence)

removes duplicate tokens in a unit sentence (i.e., tokens having the same offset position). This is necessary if abbreviations in sentence were expanded for prediction. Then, afterwards, this method needs to be called before writing the prediction into the CAS. When tokens within abbreviation long form differ in their prediction, the outside label is assumed for the abbreviation!

createUnitSentence

protected Sentence createUnitSentence(List<Token> tokenList,
                                      org.apache.uima.jcas.JCas JCas,
                                      ArrayList<HashMap<String,String>> metaList,
                                      JCoReCoverIndex<Abbreviation> abbreviationIndex,
                                      JCoReCoverIndex<Token> tokenIndex)

Takes all info about meta data and generates the corresponding unit sequence represented by a Sentence object. Abbreviation is expanded when specified in descriptor. Only abbreviations which span over single tokens can be interpreted here. Other case (which is very rare and thus probably not relevant) is ignored!

Parameters:

tokenList - a list of Token objects of the current sentence

JCas - the CAS we are working on

metaList - a Arraylist of meta-info HashMaps which specify the meta information of the respective token

abbreviationIndex -

tokenIndex -

Returns:

an array of two sequences of units containing all available meta data for the corresponding tokens. In the first sequence, abbreviations are expanded to their fullform. In the second sequence, the tokens are of their original form.

writeToCAS

public void writeToCAS(Sentence unitSentence,
                       org.apache.uima.jcas.JCas aJCas,
                       JCoReCoverIndex<Abbreviation> abbreviationIndex)

creates the respective uima annotations from JNET's predictions. Therefore, we loop over JNET's Sentence objects which contain predictions/labels for each Unit (i.e., for each token).

Parameters:

unitSentence - the current Sentence object

aJCas - the cas to write the annotation to

abbreviationIndex -

ignoreLabel

protected boolean ignoreLabel(org.apache.uima.jcas.JCas aJCas,
                              int start,
                              int end,
                              JCoReCoverIndex<Abbreviation> abbreviationIndex)

tests whether annotation should be ignored as this label is on a not introduced abbreviation

Parameters:

aJCas -

start -

end -

abbreviationIndex -

coveredText -

Returns: