public void consumeHit(JCas jcas, Annotation focusAnnot, int scope, ContextHit ctxHit) throws AnalysisEngineProcessException { if (focusAnnot instanceof IdentifiedAnnotation) { IdentifiedAnnotation neAnnot = (IdentifiedAnnotation) focusAnnot; neAnnot.setPolarity(-1); } createContextAnnot(jcas, focusAnnot, scope, ctxHit).addToIndexes(); } }
public void consumeHit(JCas jcas, Annotation focusAnnot, int scope, ContextHit ctxHit) throws AnalysisEngineProcessException { if (focusAnnot instanceof IdentifiedAnnotation) { IdentifiedAnnotation neAnnot = (IdentifiedAnnotation) focusAnnot; neAnnot.setPolarity(-1); } createContextAnnot(jcas, focusAnnot, scope, ctxHit).addToIndexes(); } }
private void checkForAttrValue(IdentifiedAnnotation eMention, String role, String value) { if (role.contains("_normalization")) { if (role.startsWith("conditional")) { eMention.setConditional(Boolean.valueOf(value)); } else if (role.startsWith("generic")) { eMention.setGeneric(Boolean.valueOf(value)); } else if (role.startsWith("negation_indicator")) { // assumes that the string from Knowtator is exactly "negation_present" if (value.equals("negation_present")) { eMention.setPolarity(CONST.NE_POLARITY_NEGATION_PRESENT); } else { eMention.setPolarity(CONST.NE_POLARITY_NEGATION_ABSENT); } } else if (role.startsWith("subject")) { // assumes that the strings from Knowtator are exactly what's in the type system eMention.setSubject(value); } else if (role.startsWith("uncertainty_indicator")) { // assumes that the string from Knowtator is exactly "indicator_present" if (value.equals("indicator_present")) { eMention.setUncertainty(CONST.NE_UNCERTAINTY_PRESENT); } else { eMention.setUncertainty(CONST.NE_UNCERTAINTY_ABSENT); } } else if (role.startsWith("generic")) { eMention.setGeneric(Boolean.valueOf(value)); } } }
private void checkForAttrValue(IdentifiedAnnotation eMention, String role, String value) { if (role.contains("_normalization")) { if (role.startsWith("conditional")) { eMention.setConditional(Boolean.valueOf(value)); } else if (role.startsWith("generic")) { eMention.setGeneric(Boolean.valueOf(value)); } else if (role.startsWith("negation_indicator")) { // assumes that the string from Knowtator is exactly "negation_present" if (value.equals("negation_present")) { eMention.setPolarity(CONST.NE_POLARITY_NEGATION_PRESENT); } else { eMention.setPolarity(CONST.NE_POLARITY_NEGATION_ABSENT); } } else if (role.startsWith("subject")) { // assumes that the strings from Knowtator are exactly what's in the type system eMention.setSubject(value); } else if (role.startsWith("uncertainty_indicator")) { // assumes that the string from Knowtator is exactly "indicator_present" if (value.equals("indicator_present")) { eMention.setUncertainty(CONST.NE_UNCERTAINTY_PRESENT); } else { eMention.setUncertainty(CONST.NE_UNCERTAINTY_ABSENT); } } else if (role.startsWith("generic")) { eMention.setGeneric(Boolean.valueOf(value)); } } }
static private void processNegatables( final String docText, final Iterable<ListEntry> listEntries, final java.util.List<IdentifiedAnnotation> negatables ) { int j = 0; IdentifiedAnnotation negatable = negatables.get( 0 ); for ( ListEntry listEntry : listEntries ) { final int entryBegin = listEntry.getBegin(); // find next negatable in a listEntry while ( negatable.getEnd() < entryBegin ) { j++; if ( j >= negatables.size() ) { return; } negatable = negatables.get( j ); } final int entryEnd = listEntry.getEnd(); // process all negatables in the current listEntry while ( negatable.getBegin() >= entryBegin && negatable.getEnd() < entryEnd ) { final String window = docText.substring( negatable.getEnd(), entryEnd ); final Matcher matcher = NEGATIVE_PATTERN.matcher( window ); if ( matcher.find() ) { negatable.setPolarity( CONST.NE_POLARITY_NEGATION_PRESENT ); } j++; if ( j >= negatables.size() ) { return; } negatable = negatables.get( j ); } } }
static private void processNegatables( final String docText, final Iterable<ListEntry> listEntries, final java.util.List<IdentifiedAnnotation> negatables ) { int j = 0; IdentifiedAnnotation negatable = negatables.get( 0 ); for ( ListEntry listEntry : listEntries ) { final int entryBegin = listEntry.getBegin(); // find next negatable in a listEntry while ( negatable.getEnd() < entryBegin ) { j++; if ( j >= negatables.size() ) { return; } negatable = negatables.get( j ); } final int entryEnd = listEntry.getEnd(); // process all negatables in the current listEntry while ( negatable.getBegin() >= entryBegin && negatable.getEnd() < entryEnd ) { final String window = docText.substring( negatable.getEnd(), entryEnd ); final Matcher matcher = NEGATIVE_PATTERN.matcher( window ); if ( matcher.find() ) { negatable.setPolarity( CONST.NE_POLARITY_NEGATION_PRESENT ); } j++; if ( j >= negatables.size() ) { return; } negatable = negatables.get( j ); } } }
.getEnd(), entityOrEventMention.getClass().getName() ) ); entityOrEventMention.setPolarity( polarity );
logger.debug(String.format("DECODING/EVAL: %s//%s [%d-%d] (%s)", label, polarity, entityOrEventMention.getBegin(), entityOrEventMention.getEnd(), entityOrEventMention.getClass().getName())); entityOrEventMention.setPolarity(polarity);
logger.debug(String.format("DECODING/EVAL: %s//%s [%d-%d] (%s)", label, polarity, entityOrEventMention.getBegin(), entityOrEventMention.getEnd(), entityOrEventMention.getClass().getName())); entityOrEventMention.setPolarity(polarity);
logger.debug(String.format("DECODING/EVAL: %s//%s [%d-%d] (%s)", label, polarity, entityOrEventMention.getBegin(), entityOrEventMention.getEnd(), entityOrEventMention.getClass().getName())); entityOrEventMention.setPolarity(polarity);
logger.debug(String.format("DECODING/EVAL: %s//%s [%d-%d] (%s)", label, polarity, entityOrEventMention.getBegin(), entityOrEventMention.getEnd(), entityOrEventMention.getClass().getName())); entityOrEventMention.setPolarity(polarity);
private void addNamedEntity(JCas jcas, int begin, int end, Map<String, OntologyConcept> concepts, boolean bMedication, Set<NegSpan> negSet) { if (concepts.isEmpty()) return; IdentifiedAnnotation neLast = bMedication ? new MedicationEventMention( jcas) : new EntityMention(jcas); neLast.setPolarity(negSet.contains(new NegSpan(begin, end)) ? CONST.NE_POLARITY_NEGATION_PRESENT : CONST.NE_POLARITY_NEGATION_ABSENT); neLast.setBegin(begin); neLast.setEnd(end); FSArray ocArr = new FSArray(jcas, concepts.size()); int ocArrIdx = 0; for (OntologyConcept oc : concepts.values()) { // set the cui field if this is in fact a cui ocArr.set(ocArrIdx, oc); ocArrIdx++; } neLast.setOntologyConceptArr(ocArr); concepts.clear(); neLast.addToIndexes(); }
private void addNamedEntity(JCas jcas, int begin, int end, Map<String, OntologyConcept> concepts, boolean bMedication, Set<NegSpan> negSet) { if (concepts.isEmpty()) return; IdentifiedAnnotation neLast = bMedication ? new MedicationEventMention( jcas) : new EntityMention(jcas); neLast.setPolarity(negSet.contains(new NegSpan(begin, end)) ? CONST.NE_POLARITY_NEGATION_PRESENT : CONST.NE_POLARITY_NEGATION_ABSENT); neLast.setBegin(begin); neLast.setEnd(end); FSArray ocArr = new FSArray(jcas, concepts.size()); int ocArrIdx = 0; for (OntologyConcept oc : concepts.values()) { // set the cui field if this is in fact a cui ocArr.set(ocArrIdx, oc); ocArrIdx++; } neLast.setOntologyConceptArr(ocArr); concepts.clear(); neLast.addToIndexes(); }
static private void fillProperties( final IdentifiedAnnotation annotation, final int polarity, final int uncertainty, final boolean generic, final boolean conditional, final String subject, final float confidence ) { annotation.setPolarity( polarity ); annotation.setUncertainty( uncertainty ); annotation.setGeneric( generic ); annotation.setConditional( conditional ); annotation.setSubject( subject ); annotation.setConfidence( confidence ); }
static private void fillProperties( final IdentifiedAnnotation annotation, final int polarity, final int uncertainty, final boolean generic, final boolean conditional, final String subject, final float confidence ) { annotation.setPolarity( polarity ); annotation.setUncertainty( uncertainty ); annotation.setGeneric( generic ); annotation.setConditional( conditional ); annotation.setSubject( subject ); annotation.setConfidence( confidence ); }
break; case POLARITY: m.setPolarity(mention.getPolarity()); break; case SUBJECT:
break; case POLARITY: m.setPolarity(mention.getPolarity()); break; case SUBJECT:
ne.setConfidence(-1); if (negated || (this.negatePossibilities && possible)) ne.setPolarity(-1); } else { ne.setPolarity(negated || possible ? -1 : 0); float confidence = negated ? -1 : 1; if (possible)
/** * * @param goldAnnotation * @param jcas */ private static void copyAnnotation(Annotation goldAnnotation, JCas jcas) { Annotation newAnno; if (goldAnnotation instanceof IdentifiedAnnotation) { IdentifiedAnnotation ia = new IdentifiedAnnotation(jcas); ia.setConditional(((IdentifiedAnnotation) goldAnnotation).getConditional()); ia.setConfidence(((IdentifiedAnnotation) goldAnnotation).getConfidence()); ia.setDiscoveryTechnique(((IdentifiedAnnotation)goldAnnotation).getDiscoveryTechnique()); ia.setGeneric(((IdentifiedAnnotation) goldAnnotation).getGeneric()); ia.setHistoryOf(((IdentifiedAnnotation) goldAnnotation).getHistoryOf()); ia.setPolarity(((IdentifiedAnnotation) goldAnnotation).getPolarity()); ia.setSegmentID(((IdentifiedAnnotation) goldAnnotation).getSegmentID()); ia.setSentenceID(((IdentifiedAnnotation) goldAnnotation).getSentenceID()); ia.setSubject(((IdentifiedAnnotation) goldAnnotation).getSubject()); ia.setTypeID(((IdentifiedAnnotation) goldAnnotation).getTypeID()); ia.setUncertainty(((IdentifiedAnnotation) goldAnnotation).getUncertainty()); newAnno = ia; } else { throw new RuntimeException("Unexpected class of object " + goldAnnotation.getClass()); } newAnno.setBegin(goldAnnotation.getBegin()); newAnno.setEnd(goldAnnotation.getEnd()); newAnno.addToIndexes(); }
/** * * @param goldAnnotation * @param jcas */ private static void copyAnnotation(Annotation goldAnnotation, JCas jcas) { Annotation newAnno; if (goldAnnotation instanceof IdentifiedAnnotation) { IdentifiedAnnotation ia = new IdentifiedAnnotation(jcas); ia.setConditional(((IdentifiedAnnotation) goldAnnotation).getConditional()); ia.setConfidence(((IdentifiedAnnotation) goldAnnotation).getConfidence()); ia.setDiscoveryTechnique(((IdentifiedAnnotation)goldAnnotation).getDiscoveryTechnique()); ia.setGeneric(((IdentifiedAnnotation) goldAnnotation).getGeneric()); ia.setHistoryOf(((IdentifiedAnnotation) goldAnnotation).getHistoryOf()); ia.setPolarity(((IdentifiedAnnotation) goldAnnotation).getPolarity()); ia.setSegmentID(((IdentifiedAnnotation) goldAnnotation).getSegmentID()); ia.setSentenceID(((IdentifiedAnnotation) goldAnnotation).getSentenceID()); ia.setSubject(((IdentifiedAnnotation) goldAnnotation).getSubject()); ia.setTypeID(((IdentifiedAnnotation) goldAnnotation).getTypeID()); ia.setUncertainty(((IdentifiedAnnotation) goldAnnotation).getUncertainty()); newAnno = ia; } else { throw new RuntimeException("Unexpected class of object " + goldAnnotation.getClass()); } newAnno.setBegin(goldAnnotation.getBegin()); newAnno.setEnd(goldAnnotation.getEnd()); newAnno.addToIndexes(); }