List of usage examples for edu.stanford.nlp.semgraph SemanticGraph vertexSet
public Set<IndexedWord> vertexSet()
From source file:de.tudarmstadt.ukp.dkpro.core.stanfordnlp.StanfordCoreferenceResolver.java
License:Open Source License
@Override public void process(JCas aJCas) throws AnalysisEngineProcessException { modelProvider.configure(aJCas.getCas()); List<Tree> trees = new ArrayList<Tree>(); List<CoreMap> sentences = new ArrayList<CoreMap>(); List<List<CoreLabel>> sentenceTokens = new ArrayList<List<CoreLabel>>(); for (ROOT root : select(aJCas, ROOT.class)) { // Copy all relevant information from the tokens List<CoreLabel> tokens = new ArrayList<CoreLabel>(); for (Token token : selectCovered(Token.class, root)) { tokens.add(tokenToWord(token)); }//from w ww . j a v a2s .co m sentenceTokens.add(tokens); // SemanticHeadFinder (nonTerminalInfo) does not know about PRN0, so we have to replace // it with PRN to avoid NPEs. TreeFactory tFact = new LabeledScoredTreeFactory(CoreLabel.factory()) { @Override public Tree newTreeNode(String aParent, List<Tree> aChildren) { String parent = aParent; if ("PRN0".equals(parent)) { parent = "PRN"; } Tree node = super.newTreeNode(parent, aChildren); return node; } }; // deep copy of the tree. These are modified inside coref! Tree treeCopy = TreeUtils.createStanfordTree(root, tFact).treeSkeletonCopy(); treeCopy.indexSpans(); trees.add(treeCopy); // Build the sentence CoreMap sentence = new CoreLabel(); sentence.set(TreeAnnotation.class, treeCopy); sentence.set(TokensAnnotation.class, tokens); sentence.set(RootKey.class, root); sentences.add(sentence); // https://code.google.com/p/dkpro-core-asl/issues/detail?id=590 // We currently do not copy over dependencies from the CAS. This is supposed to fill // in the dependencies so we do not get NPEs. TreebankLanguagePack tlp = new PennTreebankLanguagePack(); GrammaticalStructureFactory gsf = tlp.grammaticalStructureFactory(tlp.punctuationWordRejectFilter(), tlp.typedDependencyHeadFinder()); ParserAnnotatorUtils.fillInParseAnnotations(false, true, gsf, sentence, treeCopy, GrammaticalStructure.Extras.NONE); // https://code.google.com/p/dkpro-core-asl/issues/detail?id=582 SemanticGraph deps = sentence.get(SemanticGraphCoreAnnotations.CollapsedDependenciesAnnotation.class); for (IndexedWord vertex : deps.vertexSet()) { vertex.setWord(vertex.value()); } // merge the new CoreLabels with the tree leaves MentionExtractor.mergeLabels(treeCopy, tokens); MentionExtractor.initializeUtterance(tokens); } Annotation document = new Annotation(aJCas.getDocumentText()); document.set(SentencesAnnotation.class, sentences); Coreferencer coref = modelProvider.getResource(); // extract all possible mentions // Reparsing only works when the full CoreNLP pipeline system is set up! Passing false here // disables reparsing. RuleBasedCorefMentionFinder finder = new RuleBasedCorefMentionFinder(false); List<List<Mention>> allUnprocessedMentions = finder.extractPredictedMentions(document, 0, coref.corefSystem.dictionaries()); // add the relevant info to mentions and order them for coref Map<Integer, CorefChain> result; try { Document doc = coref.mentionExtractor.arrange(document, sentenceTokens, trees, allUnprocessedMentions); result = coref.corefSystem.coref(doc); } catch (Exception e) { throw new AnalysisEngineProcessException(e); } for (CorefChain chain : result.values()) { CoreferenceLink last = null; for (CorefMention mention : chain.getMentionsInTextualOrder()) { CoreLabel beginLabel = sentences.get(mention.sentNum - 1).get(TokensAnnotation.class) .get(mention.startIndex - 1); CoreLabel endLabel = sentences.get(mention.sentNum - 1).get(TokensAnnotation.class) .get(mention.endIndex - 2); CoreferenceLink link = new CoreferenceLink(aJCas, beginLabel.get(TokenKey.class).getBegin(), endLabel.get(TokenKey.class).getEnd()); if (mention.mentionType != null) { link.setReferenceType(mention.mentionType.toString()); } if (last == null) { // This is the first mention. Here we'll initialize the chain CoreferenceChain corefChain = new CoreferenceChain(aJCas); corefChain.setFirst(link); corefChain.addToIndexes(); } else { // For the other mentions, we'll add them to the chain. last.setNext(link); } last = link; link.addToIndexes(); } } }
From source file:edu.cmu.deiis.annotator.StanfordCoreNLPAnnotator.java
License:Open Source License
@Override public void process(JCas jCas) throws AnalysisEngineProcessException { Annotation document = this.processor.process(jCas.getDocumentText()); String lastNETag = "O"; int lastNEBegin = -1; int lastNEEnd = -1; for (CoreMap tokenAnn : document.get(TokensAnnotation.class)) { // create the token annotation int begin = tokenAnn.get(CharacterOffsetBeginAnnotation.class); int end = tokenAnn.get(CharacterOffsetEndAnnotation.class); String pos = tokenAnn.get(PartOfSpeechAnnotation.class); String lemma = tokenAnn.get(LemmaAnnotation.class); Token token = new Token(jCas, begin, end); token.setPos(pos);// w w w.j a v a 2s.c om token.setLemma(lemma); token.addToIndexes(); // hackery to convert token-level named entity tag into phrase-level tag String neTag = tokenAnn.get(NamedEntityTagAnnotation.class); if (neTag.equals("O") && !lastNETag.equals("O")) { NamedEntityMention ne = new NamedEntityMention(jCas, lastNEBegin, lastNEEnd); ne.setMentionType(lastNETag); ne.addToIndexes(); } else { if (lastNETag.equals("O")) { lastNEBegin = begin; } else if (lastNETag.equals(neTag)) { // do nothing - begin was already set } else { NamedEntityMention ne = new NamedEntityMention(jCas, lastNEBegin, lastNEEnd); ne.setMentionType(lastNETag); ne.addToIndexes(); lastNEBegin = begin; } lastNEEnd = end; } lastNETag = neTag; } if (!lastNETag.equals("O")) { NamedEntityMention ne = new NamedEntityMention(jCas, lastNEBegin, lastNEEnd); ne.setMentionType(lastNETag); ne.addToIndexes(); } // add sentences and trees for (CoreMap sentenceAnn : document.get(SentencesAnnotation.class)) { // add the sentence annotation int sentBegin = sentenceAnn.get(CharacterOffsetBeginAnnotation.class); int sentEnd = sentenceAnn.get(CharacterOffsetEndAnnotation.class); Sentence sentence = new Sentence(jCas, sentBegin, sentEnd); sentence.addToIndexes(); // add the syntactic tree annotation List<CoreLabel> tokenAnns = sentenceAnn.get(TokensAnnotation.class); Tree tree = sentenceAnn.get(TreeAnnotation.class); if (tree.children().length != 1) { throw new RuntimeException("Expected single root node, found " + tree); } tree = tree.firstChild(); tree.indexSpans(0); TopTreebankNode root = new TopTreebankNode(jCas); root.setTreebankParse(tree.toString()); // TODO: root.setTerminals(v) this.addTreebankNodeToIndexes(root, jCas, tree, tokenAnns); // get the dependencies SemanticGraph dependencies = sentenceAnn.get(CollapsedCCProcessedDependenciesAnnotation.class); // convert Stanford nodes to UIMA annotations List<Token> tokens = JCasUtil.selectCovered(jCas, Token.class, sentence); Map<IndexedWord, DependencyNode> stanfordToUima = new HashMap<IndexedWord, DependencyNode>(); for (IndexedWord stanfordNode : dependencies.vertexSet()) { int indexBegin = stanfordNode.get(BeginIndexAnnotation.class); int indexEnd = stanfordNode.get(EndIndexAnnotation.class); int tokenBegin = tokens.get(indexBegin).getBegin(); int tokenEnd = tokens.get(indexEnd - 1).getEnd(); DependencyNode node; if (dependencies.getRoots().contains(stanfordNode)) { node = new TopDependencyNode(jCas, tokenBegin, tokenEnd); } else { node = new DependencyNode(jCas, tokenBegin, tokenEnd); } stanfordToUima.put(stanfordNode, node); } // create relation annotations for each Stanford dependency ArrayListMultimap<DependencyNode, DependencyRelation> headRelations = ArrayListMultimap.create(); ArrayListMultimap<DependencyNode, DependencyRelation> childRelations = ArrayListMultimap.create(); for (SemanticGraphEdge stanfordEdge : dependencies.edgeIterable()) { DependencyRelation relation = new DependencyRelation(jCas); DependencyNode head = stanfordToUima.get(stanfordEdge.getGovernor()); DependencyNode child = stanfordToUima.get(stanfordEdge.getDependent()); String relationType = stanfordEdge.getRelation().toString(); if (head == null || child == null || relationType == null) { throw new RuntimeException(String.format( "null elements not allowed in relation:\nrelation=%s\nchild=%s\nhead=%s\n", relation, child, head)); } relation.setHead(head); relation.setChild(child); relation.setRelation(relationType); relation.addToIndexes(); headRelations.put(child, relation); childRelations.put(head, relation); } // set the relations for each node annotation for (DependencyNode node : stanfordToUima.values()) { List<DependencyRelation> heads = headRelations.get(node); node.setHeadRelations(new FSArray(jCas, heads == null ? 0 : heads.size())); if (heads != null) { FSCollectionFactory.fillArrayFS(node.getHeadRelations(), heads); } List<DependencyRelation> children = childRelations.get(node); node.setChildRelations(new FSArray(jCas, children == null ? 0 : children.size())); if (children != null) { FSCollectionFactory.fillArrayFS(node.getChildRelations(), children); } node.addToIndexes(); } } // map from spans to named entity mentions Map<Span, NamedEntityMention> spanMentionMap = new HashMap<Span, NamedEntityMention>(); for (NamedEntityMention mention : JCasUtil.select(jCas, NamedEntityMention.class)) { spanMentionMap.put(new Span(mention.getBegin(), mention.getEnd()), mention); } // add mentions for all entities identified by the coreference system List<NamedEntity> entities = new ArrayList<NamedEntity>(); List<List<Token>> sentenceTokens = new ArrayList<List<Token>>(); for (Sentence sentence : JCasUtil.select(jCas, Sentence.class)) { sentenceTokens.add(JCasUtil.selectCovered(jCas, Token.class, sentence)); } Map<Integer, CorefChain> corefChains = document.get(CorefChainAnnotation.class); for (CorefChain chain : corefChains.values()) { List<NamedEntityMention> mentions = new ArrayList<NamedEntityMention>(); for (CorefMention corefMention : chain.getMentionsInTextualOrder()) { // figure out the character span of the token List<Token> tokens = sentenceTokens.get(corefMention.sentNum - 1); int begin = tokens.get(corefMention.startIndex - 1).getBegin(); int end = tokens.get(corefMention.endIndex - 2).getEnd(); // use an existing named entity mention when possible; otherwise create a new one NamedEntityMention mention = spanMentionMap.get(new Span(begin, end)); if (mention == null) { mention = new NamedEntityMention(jCas, begin, end); mention.addToIndexes(); } mentions.add(mention); } // create an entity for the mentions Collections.sort(mentions, new Comparator<NamedEntityMention>() { @Override public int compare(NamedEntityMention m1, NamedEntityMention m2) { return m1.getBegin() - m2.getBegin(); } }); // create mentions and add them to entity NamedEntity entity = new NamedEntity(jCas); entity.setMentions(new FSArray(jCas, mentions.size())); int index = 0; for (NamedEntityMention mention : mentions) { mention.setMentionedEntity(entity); entity.setMentions(index, mention); index += 1; } entities.add(entity); } // add singleton entities for any named entities not picked up by coreference system for (NamedEntityMention mention : JCasUtil.select(jCas, NamedEntityMention.class)) { if (mention.getMentionedEntity() == null) { NamedEntity entity = new NamedEntity(jCas); entity.setMentions(new FSArray(jCas, 1)); entity.setMentions(0, mention); mention.setMentionedEntity(entity); entity.getMentions(); entities.add(entity); } } // sort entities by document order Collections.sort(entities, new Comparator<NamedEntity>() { @Override public int compare(NamedEntity o1, NamedEntity o2) { return getFirstBegin(o1) - getFirstBegin(o2); } private int getFirstBegin(NamedEntity entity) { int min = Integer.MAX_VALUE; for (NamedEntityMention mention : JCasUtil.select(entity.getMentions(), NamedEntityMention.class)) { if (mention.getBegin() < min) { min = mention.getBegin(); } } return min; } }); // add entities to document for (NamedEntity entity : entities) { entity.addToIndexes(); } }
From source file:edu.cmu.deiis.annotators.StanfordAnnotator.java
License:Open Source License
@Override public void process(JCas jCas) throws AnalysisEngineProcessException { Annotation document = this.processor.process(jCas.getDocumentText()); String lastNETag = "O"; int lastNEBegin = -1; int lastNEEnd = -1; for (CoreMap tokenAnn : document.get(TokensAnnotation.class)) { // create the token annotation int begin = tokenAnn.get(CharacterOffsetBeginAnnotation.class); int end = tokenAnn.get(CharacterOffsetEndAnnotation.class); String pos = tokenAnn.get(PartOfSpeechAnnotation.class); String lemma = tokenAnn.get(LemmaAnnotation.class); Token token = new Token(jCas, begin, end); token.setPos(pos);/*w w w . ja va 2 s . c o m*/ token.setLemma(lemma); token.addToIndexes(); // hackery to convert token-level named entity tag into phrase-level tag String neTag = tokenAnn.get(NamedEntityTagAnnotation.class); if (neTag.equals("O") && !lastNETag.equals("O")) { NamedEntityMention ne = new NamedEntityMention(jCas, lastNEBegin, lastNEEnd); ne.setMentionType(lastNETag); ne.addToIndexes(); } else { if (lastNETag.equals("O")) { lastNEBegin = begin; } else if (lastNETag.equals(neTag)) { // do nothing - begin was already set } else { NamedEntityMention ne = new NamedEntityMention(jCas, lastNEBegin, lastNEEnd); ne.setMentionType(lastNETag); ne.addToIndexes(); lastNEBegin = begin; } lastNEEnd = end; } lastNETag = neTag; } if (!lastNETag.equals("O")) { NamedEntityMention ne = new NamedEntityMention(jCas, lastNEBegin, lastNEEnd); ne.setMentionType(lastNETag); ne.addToIndexes(); } // add sentences and trees for (CoreMap sentenceAnn : document.get(SentencesAnnotation.class)) { // add the sentence annotation int sentBegin = sentenceAnn.get(CharacterOffsetBeginAnnotation.class); int sentEnd = sentenceAnn.get(CharacterOffsetEndAnnotation.class); Sentence sentence = new Sentence(jCas, sentBegin, sentEnd); sentence.addToIndexes(); // add the syntactic tree annotation List<CoreLabel> tokenAnns = sentenceAnn.get(TokensAnnotation.class); Tree tree = sentenceAnn.get(TreeAnnotation.class); if (tree.children().length != 1) { throw new RuntimeException("Expected single root node, found " + tree); } tree = tree.firstChild(); tree.indexSpans(0); TopTreebankNode root = new TopTreebankNode(jCas); root.setTreebankParse(tree.toString()); // TODO: root.setTerminals(v) this.addTreebankNodeToIndexes(root, jCas, tree, tokenAnns); // get the dependencies SemanticGraph dependencies = sentenceAnn.get(CollapsedCCProcessedDependenciesAnnotation.class); // convert Stanford nodes to UIMA annotations List<Token> tokens = JCasUtil.selectCovered(jCas, Token.class, sentence); Map<IndexedWord, DependencyNode> stanfordToUima = new HashMap<IndexedWord, DependencyNode>(); for (IndexedWord stanfordNode : dependencies.vertexSet()) { int indexBegin = stanfordNode.get(BeginIndexAnnotation.class); int indexEnd = stanfordNode.get(EndIndexAnnotation.class); int tokenBegin = tokens.get(indexBegin).getBegin(); int tokenEnd = tokens.get(indexEnd - 1).getEnd(); DependencyNode node; if (dependencies.getRoots().contains(stanfordNode)) { node = new TopDependencyNode(jCas, tokenBegin, tokenEnd); } else { node = new DependencyNode(jCas, tokenBegin, tokenEnd); } stanfordToUima.put(stanfordNode, node); } // create relation annotations for each Stanford dependency ArrayListMultimap<DependencyNode, DependencyRelation> headRelations = ArrayListMultimap.create(); ArrayListMultimap<DependencyNode, DependencyRelation> childRelations = ArrayListMultimap.create(); for (SemanticGraphEdge stanfordEdge : dependencies.edgeIterable()) { DependencyRelation relation = new DependencyRelation(jCas); DependencyNode head = stanfordToUima.get(stanfordEdge.getGovernor()); DependencyNode child = stanfordToUima.get(stanfordEdge.getDependent()); String relationType = stanfordEdge.getRelation().toString(); if (head == null || child == null || relationType == null) { throw new RuntimeException(String.format( "null elements not allowed in relation:\nrelation=%s\nchild=%s\nhead=%s\n", relation, child, head)); } relation.setHead(head); relation.setChild(child); relation.setRelation(relationType); relation.addToIndexes(); headRelations.put(child, relation); childRelations.put(head, relation); } // set the relations for each node annotation for (DependencyNode node : stanfordToUima.values()) { List<DependencyRelation> heads = headRelations.get(node); node.setHeadRelations(new FSArray(jCas, heads == null ? 0 : heads.size())); if (heads != null) { FSCollectionFactory.fillArrayFS(node.getHeadRelations(), heads); } List<DependencyRelation> children = childRelations.get(node); node.setChildRelations(new FSArray(jCas, children == null ? 0 : children.size())); if (children != null) { FSCollectionFactory.fillArrayFS(node.getChildRelations(), children); } node.addToIndexes(); } } // map from spans to named entity mentions Map<Span, NamedEntityMention> spanMentionMap = new HashMap<Span, NamedEntityMention>(); for (NamedEntityMention mention : JCasUtil.select(jCas, NamedEntityMention.class)) { spanMentionMap.put(new Span(mention.getBegin(), mention.getEnd()), mention); } // add mentions for all entities identified by the coreference system List<NamedEntity> entities = new ArrayList<NamedEntity>(); List<List<Token>> sentenceTokens = new ArrayList<List<Token>>(); for (Sentence sentence : JCasUtil.select(jCas, Sentence.class)) { sentenceTokens.add(JCasUtil.selectCovered(jCas, Token.class, sentence)); } Map<Integer, CorefChain> corefChains = document.get(CorefChainAnnotation.class); for (CorefChain chain : corefChains.values()) { List<NamedEntityMention> mentions = new ArrayList<NamedEntityMention>(); for (CorefMention corefMention : chain.getMentionsInTextualOrder()) { // figure out the character span of the token List<Token> tokens = sentenceTokens.get(corefMention.sentNum - 1); int begin = tokens.get(corefMention.startIndex - 1).getBegin(); int end = tokens.get(corefMention.endIndex - 2).getEnd(); // use an existing named entity mention when possible; otherwise create a new one NamedEntityMention mention = spanMentionMap.get(new Span(begin, end)); if (mention == null) { mention = new NamedEntityMention(jCas, begin, end); //String line = mention.getCoveredText(); //System.out.println(line); mention.addToIndexes(); } mentions.add(mention); } // create an entity for the mentions Collections.sort(mentions, new Comparator<NamedEntityMention>() { @Override public int compare(NamedEntityMention m1, NamedEntityMention m2) { return m1.getBegin() - m2.getBegin(); } }); // create mentions and add them to entity NamedEntity entity = new NamedEntity(jCas); entity.setMentions(new FSArray(jCas, mentions.size())); int index = 0; for (NamedEntityMention mention : mentions) { mention.setMentionedEntity(entity); entity.setMentions(index, mention); index += 1; } entities.add(entity); } // add singleton entities for any named entities not picked up by coreference system for (NamedEntityMention mention : JCasUtil.select(jCas, NamedEntityMention.class)) { if (mention.getMentionedEntity() == null) { NamedEntity entity = new NamedEntity(jCas); entity.setMentions(new FSArray(jCas, 1)); entity.setMentions(0, mention); mention.setMentionedEntity(entity); entity.getMentions(); entities.add(entity); } } // sort entities by document order Collections.sort(entities, new Comparator<NamedEntity>() { @Override public int compare(NamedEntity o1, NamedEntity o2) { return getFirstBegin(o1) - getFirstBegin(o2); } private int getFirstBegin(NamedEntity entity) { int min = Integer.MAX_VALUE; for (NamedEntityMention mention : JCasUtil.select(entity.getMentions(), NamedEntityMention.class)) { if (mention.getBegin() < min) { min = mention.getBegin(); } } return min; } }); // add entities to document for (NamedEntity entity : entities) { //NamedEntityMention mention=entity.getMentions(3); //System.out.println(mention.getBegin()); entity.addToIndexes(); } }
From source file:org.textmining.annotator.StanfordCoreNlpAnnotator.java
License:Open Source License
@Override public void process(JCas jCas) throws AnalysisEngineProcessException { Annotation document = this.processor.process(jCas.getDocumentText()); String lastNETag = "O"; int lastNEBegin = -1; int lastNEEnd = -1; for (CoreMap tokenAnn : document.get(TokensAnnotation.class)) { // create the token annotation int begin = tokenAnn.get(CharacterOffsetBeginAnnotation.class); int end = tokenAnn.get(CharacterOffsetEndAnnotation.class); String pos = tokenAnn.get(PartOfSpeechAnnotation.class); String lemma = tokenAnn.get(LemmaAnnotation.class); Token token = new Token(jCas, begin, end); token.setPos(pos);/*from ww w . j av a 2s.c om*/ token.setLemma(lemma); token.addToIndexes(); // hackery to convert token-level named entity tag into phrase-level tag String neTag = tokenAnn.get(NamedEntityTagAnnotation.class); if (neTag.equals("O") && !lastNETag.equals("O")) { NamedEntityMention ne = new NamedEntityMention(jCas, lastNEBegin, lastNEEnd); ne.setMentionType(lastNETag); ne.addToIndexes(); } else { if (lastNETag.equals("O")) { lastNEBegin = begin; } else if (lastNETag.equals(neTag)) { // do nothing - begin was already set } else { NamedEntityMention ne = new NamedEntityMention(jCas, lastNEBegin, lastNEEnd); ne.setMentionType(lastNETag); ne.addToIndexes(); lastNEBegin = begin; } lastNEEnd = end; } lastNETag = neTag; } if (!lastNETag.equals("O")) { NamedEntityMention ne = new NamedEntityMention(jCas, lastNEBegin, lastNEEnd); ne.setMentionType(lastNETag); ne.addToIndexes(); } // add sentences and trees for (CoreMap sentenceAnn : document.get(SentencesAnnotation.class)) { // add the sentence annotation int sentBegin = sentenceAnn.get(CharacterOffsetBeginAnnotation.class); int sentEnd = sentenceAnn.get(CharacterOffsetEndAnnotation.class); Sentence sentence = new Sentence(jCas, sentBegin, sentEnd); sentence.addToIndexes(); // add the syntactic tree annotation List<CoreLabel> tokenAnns = sentenceAnn.get(TokensAnnotation.class); Tree tree = sentenceAnn.get(TreeAnnotation.class); if (tree.children().length != 1) { throw new RuntimeException("Expected single root node, found " + tree); } tree = tree.firstChild(); tree.indexSpans(0); TopTreebankNode root = new TopTreebankNode(jCas); root.setTreebankParse(tree.toString()); // TODO: root.setTerminals(v) this.addTreebankNodeToIndexes(root, jCas, tree, tokenAnns); // get the dependencies SemanticGraph dependencies = sentenceAnn.get(CollapsedCCProcessedDependenciesAnnotation.class); // convert Stanford nodes to UIMA annotations List<Token> tokens = JCasUtil.selectCovered(jCas, Token.class, sentence); Map<IndexedWord, DependencyNode> stanfordToUima = new HashMap<IndexedWord, DependencyNode>(); for (IndexedWord stanfordNode : dependencies.vertexSet()) { int indexBegin = stanfordNode.get(BeginIndexAnnotation.class); int indexEnd = stanfordNode.get(EndIndexAnnotation.class); int tokenBegin = tokens.get(indexBegin).getBegin(); int tokenEnd = tokens.get(indexEnd - 1).getEnd(); DependencyNode node; if (dependencies.getRoots().contains(stanfordNode)) { node = new TopDependencyNode(jCas, tokenBegin, tokenEnd); } else { node = new DependencyNode(jCas, tokenBegin, tokenEnd); } stanfordToUima.put(stanfordNode, node); } // create relation annotations for each Stanford dependency ArrayListMultimap<DependencyNode, DependencyRelation> headRelations = ArrayListMultimap.create(); ArrayListMultimap<DependencyNode, DependencyRelation> childRelations = ArrayListMultimap.create(); for (SemanticGraphEdge stanfordEdge : dependencies.edgeIterable()) { DependencyRelation relation = new DependencyRelation(jCas); DependencyNode head = stanfordToUima.get(stanfordEdge.getGovernor()); DependencyNode child = stanfordToUima.get(stanfordEdge.getDependent()); String relationType = stanfordEdge.getRelation().toString(); if (head == null || child == null || relationType == null) { throw new RuntimeException(String.format( "null elements not allowed in relation:\nrelation=%s\nchild=%s\nhead=%s\n", relation, child, head)); } relation.setHead(head); relation.setChild(child); relation.setRelation(relationType); relation.addToIndexes(); headRelations.put(child, relation); childRelations.put(head, relation); } // set the relations for each node annotation for (DependencyNode node : stanfordToUima.values()) { List<DependencyRelation> heads = headRelations.get(node); node.setHeadRelations(new FSArray(jCas, heads == null ? 0 : heads.size())); if (heads != null) { FSCollectionFactory.fillArrayFS(node.getHeadRelations(), heads); } List<DependencyRelation> children = childRelations.get(node); node.setChildRelations(new FSArray(jCas, children == null ? 0 : children.size())); if (children != null) { FSCollectionFactory.fillArrayFS(node.getChildRelations(), children); } node.addToIndexes(); } } // map from spans to named entity mentions Map<Span, NamedEntityMention> spanMentionMap = new HashMap<Span, NamedEntityMention>(); for (NamedEntityMention mention : JCasUtil.select(jCas, NamedEntityMention.class)) { spanMentionMap.put(new Span(mention.getBegin(), mention.getEnd()), mention); } // add mentions for all entities identified by the coreference system List<NamedEntity> entities = new ArrayList<NamedEntity>(); List<List<Token>> sentenceTokens = new ArrayList<List<Token>>(); for (Sentence sentence : JCasUtil.select(jCas, Sentence.class)) { sentenceTokens.add(JCasUtil.selectCovered(jCas, Token.class, sentence)); } Map<Integer, CorefChain> corefChains = document.get(CorefChainAnnotation.class); for (CorefChain chain : corefChains.values()) { List<NamedEntityMention> mentions = new ArrayList<NamedEntityMention>(); for (CorefMention corefMention : chain.getMentionsInTextualOrder()) { // figure out the character span of the token List<Token> tokens = sentenceTokens.get(corefMention.sentNum - 1); int begin = tokens.get(corefMention.startIndex - 1).getBegin(); int end = tokens.get(corefMention.endIndex - 2).getEnd(); // use an existing named entity mention when possible; otherwise create a new one NamedEntityMention mention = spanMentionMap.get(new Span(begin, end)); if (mention == null) { mention = new NamedEntityMention(jCas, begin, end); mention.addToIndexes(); } mentions.add(mention); } // create an entity for the mentions Collections.sort(mentions, new Comparator<NamedEntityMention>() { @Override public int compare(NamedEntityMention m1, NamedEntityMention m2) { return m1.getBegin() - m2.getBegin(); } }); // create mentions and add them to entity NamedEntity entity = new NamedEntity(jCas); entity.setMentions(new FSArray(jCas, mentions.size())); int index = 0; for (NamedEntityMention mention : mentions) { mention.setMentionedEntity(entity); entity.setMentions(index, mention); index += 1; } entities.add(entity); } // add singleton entities for any named entities not picked up by coreference system for (NamedEntityMention mention : JCasUtil.select(jCas, NamedEntityMention.class)) { if (mention.getMentionedEntity() == null) { NamedEntity entity = new NamedEntity(jCas); entity.setMentions(new FSArray(jCas, 1)); entity.setMentions(0, mention); mention.setMentionedEntity(entity); entity.getMentions(); entities.add(entity); } } // sort entities by document order Collections.sort(entities, new Comparator<NamedEntity>() { @Override public int compare(NamedEntity o1, NamedEntity o2) { return getFirstBegin(o1) - getFirstBegin(o2); } private int getFirstBegin(NamedEntity entity) { int min = Integer.MAX_VALUE; for (NamedEntityMention mention : JCasUtil.select(entity.getMentions(), NamedEntityMention.class)) { if (mention.getBegin() < min) { min = mention.getBegin(); } } return min; } }); // add entities to document for (NamedEntity entity : entities) { entity.addToIndexes(); } //end of process-method }