Index (BioSem Event Extractor 1.1.6 API)

A B C D E F G H I K L M N O P R S T U V W

A

abs2Sen(String, String) - Method in class relations.SenSimplifier: Deprecated.
add(int) - Method in class relations.Counter
addChunk(BasicChunk) - Method in class relations.BasicChunk
addChunk(Chunk) - Method in class relations.BasicChunk
addPattern(int, String, String, boolean, String, boolean, int, String, boolean) - Method in class relations.Rules: For simple events
addPattern(int, String, String, boolean, boolean, boolean, String, String, boolean, boolean, int, int, String, boolean) - Method in class relations.Rules: Binding events
addPattern(int, String, String, boolean, boolean, boolean, String, String, boolean, boolean, int, int, boolean, boolean, String, String, boolean) - Method in class relations.Rules: Regulatory events
addPro(Word) - Method in class relations.BasicChunk
addPro(Word) - Method in class relations.Chunk: Add protein
addToMap(KeyData) - Method in class relations.KeyData: Add shared/mix trigger to map
addTrg(Word) - Method in class relations.BasicChunk
addTrigger(Word) - Method in class relations.Chunk: Add trigger
addVerb(Chunk) - Method in class relations.VerbChunk
addWord(String) - Method in class relations.Chunk
allMap - Variable in class relations.ChunkAnalyzer
analyze(String) - Method in class relations.SenAnalyzer: Main method to analyze text
analyzeChunk(List<Chunk>, String[], String[]) - Method in class relations.ChunkAnalyzer: Analyzing chunks to form NP, VP...
application - package application
applyScore() - Method in class relations.RuleSet
appoList - Static variable in class relations.BasicChunk
appoMap - Static variable in class relations.BasicChunk
appoMap - Variable in class relations.ChunkAnalyzer

B

BasicChunk - Class in relations
BasicChunk() - Constructor for class relations.BasicChunk
begin - Variable in class relations.Chunk
begin - Variable in class utils.SentenceSplitter.BioSemSentence
belongTO(Word, Word) - Method in class relations.BasicChunk
belongTO(Word, Word, Word) - Method in class relations.BasicChunk
belongTO(Word, Word) - Method in class relations.VerbChunk: For simple events/ or binding without theme2
belongTO(Word, Word, Word) - Method in class relations.VerbChunk
beMap - Variable in class relations.ChunkAnalyzer
BioSemApplication - Class in application
BioSemApplication() - Constructor for class application.BioSemApplication
BioSemException - Exception in utils
BioSemException(Exception) - Constructor for exception utils.BioSemException
breakMap - Variable in class relations.ChunkAnalyzer
brLine(String, String) - Method in class relations.SenSimplifier: Used to split the text after the title which often does not end with a full stop, this posing an issue for the sentence splitter.

C

cause - Variable in class relations.Chunk
cause - Variable in class relations.Word
ccList - Static variable in class relations.BasicChunk
ccList - Static variable in class relations.EventExtraction
ccMap - Static variable in class relations.BasicChunk
ccMap - Variable in class relations.ChunkAnalyzer
ccSet - Static variable in class relations.EventExtraction
checkTable(String) - Method in class utils.DBUtils: Check if a table already exists
child - Variable in class relations.TriggerLearner.TriggerData
childMap - Variable in class relations.RuleData
Chunk - Class in relations
Chunk(String) - Constructor for class relations.Chunk
chunk_type - Variable in class relations.Word
ChunkAnalyzer - Class in relations: Define all operations on Chunk such as forming NP, VP, PP, AP
ChunkAnalyzer() - Constructor for class relations.ChunkAnalyzer
cleanChunk(List<Chunk>, String[], String[]) - Method in class relations.ChunkAnalyzer
clearList() - Method in class relations.TriggerLearner
close() - Method in class corpora.DataSaver
closeDB() - Method in class relations.SenAnalyzer: Close database [never called]
closeDB() - Method in class relations.SenSimplifier
closeDB() - Method in class utils.DBUtils
combined - Variable in class relations.Word
combiningRules(Map<String, Rules>[]) - Method in class relations.RuleLearner
comparePatterns() - Method in class relations.Eval
compareTo(Object) - Method in class relations.Counter
compareTo(Object) - Method in class relations.KeyData
compareTo(Object) - Method in class relations.PData
compareTo(Object) - Method in class relations.RuleData
compareTo(Object) - Method in class relations.TData
compareTo(Object) - Method in class relations.Word
compound - Variable in class relations.Word
con - Variable in class utils.DBUtils
contains(Word) - Method in class relations.Chunk
containsKey(Word) - Method in class relations.BasicChunk
corpora - package corpora
count - Variable in class relations.Counter
count_chunk - Variable in class relations.ChunkAnalyzer
countChunks(Word, Word) - Method in class relations.BasicChunk
Counter - Class in relations
Counter(int) - Constructor for class relations.Counter
Counter() - Constructor for class relations.Counter
countLevel() - Method in class relations.Eval
createRule(List<RuleData>) - Method in class relations.RuleSets: Split of pattern into defined group
createTriggers() - Method in class relations.TriggerLearner: Creating trigger list from training data
cscore - Variable in class relations.KeyData
curr_text - Variable in class relations.ChunkAnalyzer

D

DataLoader - Class in corpora
DataLoader() - Constructor for class corpora.DataLoader
DataSaver - Class in corpora
DataSaver(DBUtils) - Constructor for class corpora.DataSaver
DBUtils - Class in utils
DBUtils() - Constructor for class utils.DBUtils
DBUtils(String, String) - Constructor for class utils.DBUtils
DBUtils(String, String, String) - Constructor for class utils.DBUtils
detectTrg(String) - Method in class relations.SenAnalyzer
DictEval() - Method in class relations.Eval: Evaluating dictionary
doSentenceSplitting(String, String) - Method in class relations.SenSimplifier
doSimplify() - Method in class relations.SenSimplifier: Deprecated.
doSimplifySentenceWise(SentenceSplitter.BioSemSentence[], List<TData>) - Method in class relations.SenSimplifier
dropTable(String) - Method in class utils.DBUtils

E

EData - Class in relations
EData(String, String, String, String, String, String, String) - Constructor for class relations.EData
end - Variable in class relations.Chunk
end - Variable in class utils.SentenceSplitter.BioSemSentence
equiList - Variable in class relations.SenSimplifier
equimap - Variable in class relations.SenSimplifier
er_count - Variable in class relations.SenSimplifier: Check whether this sentence qualify for extracting event
escore - Variable in class relations.KeyData
Eval - Class in relations
Eval() - Constructor for class relations.Eval: Main class for extracting event from text
Eval(SenSimplifier) - Constructor for class relations.Eval
evalReg() - Method in class relations.Eval
evalSimple() - Method in class relations.Eval
evaluateTrg(BasicChunk, List<Word>, List<Word>, String[], List<Word>) - Method in class relations.EventExtraction: Evaluating candidate triggers whether they can form events
EventExtraction - Class in relations
EventExtraction(DBUtils, DBUtils) - Constructor for class relations.EventExtraction: Extract event from the given data
evt_type - Variable in class relations.PData
evtMap - Variable in class relations.Eval
execUpdate(String) - Method in class utils.DBUtils
extractBindNP(Word, BasicChunk, List<Word>) - Method in class relations.EventExtraction: 12.10.2011 Extracting binding events
extractBindVP(Word, VerbChunk, List<Word>) - Method in class relations.EventExtraction
extracted - Variable in class relations.BasicChunk
extracted - Variable in class relations.RuleData
extractEvents(String) - Method in class relations.EventExtraction: Extracting events from abstract/paragraph.
extractNP(BasicChunk, List<Word>) - Method in class relations.EventExtraction
extractNP(int, BasicChunk, List<Word>) - Method in class relations.EventExtraction
extractRegNP(Word, BasicChunk, List<Word>) - Method in class relations.EventExtraction
extractRegVP(Word, VerbChunk, List<Word>) - Method in class relations.EventExtraction
extractSentence(int) - Method in class relations.EventExtraction
extractSimpleNP(Word, BasicChunk, List<Word>) - Method in class relations.EventExtraction: Extracting simple event from BasicChunk with a given trigger (+type)
extractSimpleVP(Word, VerbChunk, List<Word>) - Method in class relations.EventExtraction: Find pros for binding event which has pattern as: Pro1 - Trg - Pro2
extractVP(VerbChunk, List<Word>, List<Word>) - Method in class relations.EventExtraction
extraMap - Variable in class relations.ChunkAnalyzer

F

findCausePro(BasicChunk, Word) - Method in class relations.EventExtraction: Get Pro as cause for : PRO-xx TG PRO/EVENT
findCoordinator(List<Chunk>) - Method in class relations.BasicChunk
findEquiv(String) - Method in class relations.SenAnalyzer: DO NOT USE! This method is not correct due to some changes.
findFrontPro(BasicChunk, Word, int) - Method in class relations.EventExtraction: 12.10.2011 Find pro in front of tg for noun phrase/subject patterns: PRO - TG
findObject(int, List<Chunk>, int) - Method in class relations.ChunkAnalyzer
findPos(int[], Word[]) - Method in class relations.Eval
findPreviousNP(BasicChunk) - Method in class relations.ChunkAnalyzer: For 'which' and 'that' relative clause
findPro(BasicChunk, Word, String, int) - Method in class relations.EventExtraction: 11.10.2011.
findPro(BasicChunk, int, int) - Method in class relations.EventExtraction: Find pro after a given position (for use with tg- prep1 - prep2) Only looks for pro after prep2
findProIndex(List<TData>, int) - Method in class relations.SenSimplifier
findRegPro(BasicChunk, Word, int, int) - Method in class relations.EventExtraction: Find pro after a given position (for use with tg- prep1 - prep2) Only looks for pro after prep2
findSubject(int, List<Chunk>, int) - Method in class relations.ChunkAnalyzer
findTrigger(Word, Word) - Method in class relations.BasicChunk
findTrigger(int[], List<Word>) - Method in class relations.SenAnalyzer
fullword - Variable in class relations.Word

G

generateKeyData() - Method in class relations.TriggerLearner
genia_tag - Variable in class parser.Parser
getBehindScore() - Method in class relations.RuleSets: Score of event having theme behind TG ; for simple event only; TODO: for other events need to take into account group 6
getBy_Through(Word, Word, String[]) - Method in class relations.BasicChunk
getCause() - Method in class relations.EData
getCauseScore() - Method in class relations.RuleSet: Ratio of event has cause
getCauseScore() - Method in class relations.RuleSets: Get score of an event having cause/theme2.
getChunk(int) - Method in class relations.BasicChunk
getChunkPos(int) - Method in class relations.BasicChunk
getConnection() - Method in class utils.DBUtils: Unused
getDb_root() - Method in class application.BioSemApplication
getDefault() - Method in class relations.KeyData: Get default event type (ignoring modifiers) In this case, use the highest frequency as default type
getDestination() - Method in class application.BioSemApplication
getEv2Score() - Method in class relations.RuleSet: Ratio of event as cause
getEvalRules(String) - Method in class relations.Rules: Get list of patterns
getEvtCause(int) - Method in class relations.RuleSets: Get score of an event having cause as an event
getEvtScore() - Method in class relations.RuleSet: Ratio of event as theme
getEvtScore(int) - Method in class relations.RuleSets: Get score of an event having theme as an event
getExtractedEvents() - Method in class relations.EventExtraction: Available after EventExtraction.Test() or EventExtraction.Test(String) has been run.
getExtractedTriggers() - Method in class relations.EventExtraction: Available after EventExtraction.Test() or EventExtraction.Test(String) has been run.
getFreq() - Method in class relations.RuleSet: Count frequency of this rule, should not use alone, use getScore instead.
getFrontScore() - Method in class relations.RuleSets: Score of event having theme infront of TG
getInchunkCause() - Method in class relations.RuleSets
getInChunkEvtScore() - Method in class relations.RuleSets
getInChunkPro(Word, String[]) - Method in class relations.Chunk: Get in_chunk pro for a given tg
getInChunkPro(BasicChunk, Word) - Method in class relations.EventExtraction: 11.10.2011.
getInput_root() - Method in class application.BioSemApplication
getKey() - Method in class relations.RuleData
getKeyData(String) - Method in class relations.KeyData: get KeyData for shared and mixed trigger
getKeyInfo() - Method in class relations.RuleData
getLevel(int) - Method in class relations.EData
getMap() - Method in class relations.KeyData: get list of shared /mix trigger -> which has the same key
getMod(Chunk, Chunk, List<Word>) - Method in class relations.EventExtraction: Get modifier for trigger in order to determine trigger type
getMod(int, int, List<Word>) - Method in class relations.EventExtraction: Get modifier for trigger in order to determine trigger type
getMod(BasicChunk, Word, List<Word>) - Method in class relations.EventExtraction: Get modifier for trigger in order to determine trigger type
getMod(BasicChunk, Word, List<Word>, List<Word>) - Method in class relations.EventExtraction: Get modifier for trigger in order to determine trigger type
getModifier(String[]) - Method in class relations.SenAnalyzer: Get list of prepositions of a sentence
getModus() - Method in class application.BioSemApplication
getOffset(int, int[]) - Method in class relations.SenSimplifier
getPdata1() - Method in class relations.PData
getPdata2() - Method in class relations.PData
getPIndex(String) - Method in class relations.SenSimplifier
getPrep(Word, Word) - Method in class relations.BasicChunk
getPrep(Word, Word, BasicChunk) - Method in class relations.RuleLearner
getPrep2(Word, Word, BasicChunk) - Method in class relations.RuleLearner
getPrepFront(Word, Word, BasicChunk) - Method in class relations.RuleLearner
getPreps(String[]) - Method in class relations.SenAnalyzer: Get list of prepositions of a sentence
getPro() - Method in class relations.BasicChunk
getPro(String[]) - Method in class relations.Chunk: 12.10.2011 Get pro list in form TG_PRO for strict case (no other trigger in between)
getPro(Word, String[]) - Method in class relations.Chunk: Get pros (same chunk with trg) that follow the given trigger for pattern: TG - PR This method is used in case there is no prep or trg has JJ/VBx form in noun chunk
getPro() - Method in class relations.EData: Get protein closest to the trigger in order to map trigger location into sentence and vice vesa
getPro1() - Method in class relations.PData
getPro2() - Method in class relations.PData
getProCause(int) - Method in class relations.RuleSets: Get score of an event having cause as an pro
getProFront() - Method in class relations.Chunk: 12.10.2011 Get pro list for strict case (no other trigger in between)
getProScore(int) - Method in class relations.RuleSets: Get score of an event having theme as an pro
getProtein() - Method in class relations.PData
getProteins(String) - Method in class relations.SenSimplifier
getScore() - Method in class relations.RuleSet: Confident score for this rule, if this value is low, skip this rule
getSenIndex(int, int[]) - Method in class relations.SenSimplifier
getSet() - Method in class application.BioSemApplication
getSubKey() - Method in class relations.RuleData
getT1Score() - Method in class relations.RuleSet: For binding only; this value is used to determine whether to use pro in front of TG as theme/ or use t2 score
getT2Score() - Method in class relations.RuleSet: Theme 2 score
getText() - Method in class relations.Chunk
getText() - Method in class relations.PData
getTrigger() - Method in class relations.EData
getTrigger() - Method in class relations.PData
getTxt(int) - Method in class relations.EData
getTxt() - Method in class relations.EData
getType() - Method in class relations.Chunk
getType() - Method in class relations.EData
getType(List<Word>) - Method in class relations.KeyData: Determine event type based on a given list of modifiers
getValue() - Method in class relations.Counter
getValues() - Method in class relations.Chunk
getVerbChunkType(Chunk) - Method in class relations.ChunkAnalyzer: Determine verb chunk type: passive/active/gerund
getWriteID() - Method in class relations.PData
groupRules(Map<String, Rules>[]) - Method in class relations.EventExtraction

H

hashType - Static variable in class relations.SenSimplifier

I

id - Variable in class parser.Parser
inc() - Method in class relations.Counter
inChunk(Word, Word) - Method in class relations.BasicChunk
inChunk(Word, Word) - Method in class relations.Chunk: Check TG and Pro in the same chunk, for use with learning rules
inChunk(Word, Word, String[]) - Method in class relations.Chunk: Check TG and Pro in the same chunk, for use with learning rules
inChunk() - Method in class relations.RuleSets: Check whether this pattern has inchunk form
inchunk - Variable in class relations.Word
inchunkScore() - Method in class relations.RuleSet: Percentage of event has in chunk form, if this value is low, then skip in-chunk event
inChunkTG(Word, Word) - Method in class relations.BasicChunk: Two tg in the same chunk ; for learning rule only
inChunkTG(Word, Word) - Method in class relations.Chunk: Check two trg in the same chunk, without any pro in between of them
inChunkTrg(Word, String[]) - Method in class relations.BasicChunk: Check whether a given trigger is in_chunk form
init - Variable in class relations.BasicChunk
init(Map<String, TData>, Map<String, TData>, Map<String, EData>) - Method in class relations.EData
init() - Method in class relations.EventExtraction
init - Variable in class relations.KeyData
init() - Method in class relations.SenAnalyzer: Loading dictionaries
initAbstract(String) - Method in class relations.Eval: Load all data (protein, trigger, event) belong to this abtract/paragraph Split abstract/paragraph into sentences
initAbstract(String) - Method in class relations.SenAnalyzer
initData(String, String) - Method in class relations.KeyData
initData(String) - Method in class relations.SenAnalyzer: Workflow: 1.
initEventData(String) - Method in class relations.TriggerLearner
initMap() - Method in class relations.Rules
initParser() - Method in class parser.Parser
initSentence(String) - Method in class relations.EventExtraction
is_a_Map - Variable in class relations.ChunkAnalyzer
is_a_phrase(Chunk) - Method in class relations.ChunkAnalyzer
is_inChunk(Word, String[]) - Method in class relations.Chunk: Check whether a trg has in_chunk form
is_merged - Variable in class relations.BasicChunk
is_merged - Variable in class relations.Chunk
is_passive(Chunk) - Method in class relations.ChunkAnalyzer
isEmpty() - Method in class relations.BasicChunk: Check whether this basic chunk is empty.
isQualify() - Method in class relations.BasicChunk
isQualify() - Method in class relations.Chunk
isQualify() - Method in class relations.VerbChunk
isSameChunk(Word, Word) - Method in class relations.BasicChunk: Check whether in the same chunk but not in_chunk form
isSameRole(Word, Word, String[]) - Method in class relations.BasicChunk: Check whether two trigger has the same role (i.e have the same arguments)
isSameRole(Word, Word, String[]) - Method in class relations.Chunk
isSkipped() - Method in class relations.RuleSets: Check whether to skip this pattern
isSkipped(int) - Method in class relations.RuleSets: Check whether to skip this pattern

K

KeyData - Class in relations
KeyData(String, String, int, int, int) - Constructor for class relations.KeyData
keytype - Variable in class relations.Word

L

LearnData() - Method in class relations.RuleLearner
loadData(String, boolean) - Method in class corpora.DataLoader
loadDict(DBUtils) - Method in class relations.SenSimplifier: Load dictionary from default database DB: DB source to load dictionary
loadEquiv(String) - Method in class relations.SenSimplifier
loadEvent(String) - Method in class relations.SenSimplifier
loadPatterns(DBUtils) - Method in class relations.SenSimplifier: Load pattern from database
loadPMIDs() - Method in class relations.SenSimplifier: Load abstract ID from database
loadProtein(String) - Method in class relations.SenSimplifier
loadRuleSet(DBUtils) - Method in class relations.SenSimplifier
loadSentence(String) - Method in class relations.SenSimplifier
loadSimpleDic(Map<String, KeyData>) - Method in class relations.SenSimplifier
loadSimpleDic() - Method in class relations.SenSimplifier
loadSimplified(String) - Method in class relations.SenSimplifier: Deprecated.
loadTrigger(String) - Method in class relations.SenSimplifier
loc - Variable in class relations.Word
locs - Variable in class relations.Word

M

main(String[]) - Static method in class application.BioSemApplication
main(String[]) - Static method in class corpora.DataLoader
main(String[]) - Static method in class parser.Parser
main(String[]) - Static method in class relations.ChunkAnalyzer
main(String[]) - Static method in class relations.Eval
main(String[]) - Static method in class relations.EventExtraction
main(String[]) - Static method in class relations.RuleLearner
main(String[]) - Static method in class relations.SenAnalyzer
main(String[]) - Static method in class relations.SenSimplifier
main(String[]) - Static method in class relations.TriggerLearner
main(String[]) - Static method in class utils.SentenceSplitter
mapToStr(Map<String, Set<String>>) - Method in class relations.RuleLearner
mapToString(Set<String>) - Method in class relations.RuleData
merge(Chunk) - Method in class relations.Chunk: Merge two chunks: appending a chunk to the current chunk
merge() - Method in class relations.VerbChunk: Merge this verb chunk to create BasicChunk
mergeNP() - Method in class relations.BasicChunk
modifiers - Static variable in class relations.SenSimplifier

N

none_rel - Static variable in class relations.SenSimplifier
none_rel - Static variable in class relations.TriggerLearner
nr_event - Variable in class relations.SenSimplifier

O

old_txt - Variable in class parser.Parser
openDB() - Method in class utils.DBUtils
openDB(String) - Method in class utils.DBUtils

P

parent - Variable in class relations.TriggerLearner.TriggerData
parentMap - Variable in class relations.RuleData
parse(String[]) - Method in class parser.Parser: Shallow parser: generating chunks (NP,VP, PP) from untokenized text
parse(String[], String[]) - Method in class parser.Parser
parser - package parser
Parser - Class in parser
Parser() - Constructor for class parser.Parser
PData - Class in relations
PData(Word, Object, String) - Constructor for class relations.PData
PData(Word, Object, Object, String) - Constructor for class relations.PData
PID - Variable in class relations.PData
pos - Variable in class relations.Word
pos_tag - Variable in class relations.Word
POSTag(String[]) - Method in class parser.Parser: Tag a list of tokens with POS
preparedData() - Method in class relations.TriggerLearner: Read raw data from tables, generate statistical values
prepList - Static variable in class relations.EventExtraction
prepMap - Variable in class relations.ChunkAnalyzer
prepmap - Static variable in class relations.RuleLearner
prepmap - Static variable in class relations.SenSimplifier
preps - Static variable in class relations.RuleLearner
preps - Static variable in class relations.SenSimplifier
prepSet - Static variable in class relations.EventExtraction
prepWord - Variable in class relations.TriggerLearner
print() - Method in class relations.VerbChunk
print_chunk - Variable in class relations.ChunkAnalyzer
printAllSentence(int) - Method in class relations.Eval
printChunk(String) - Method in class parser.Parser
printChunk(List<Chunk>) - Method in class parser.Parser
printChunk() - Method in class relations.BasicChunk
printChunk(List<Chunk>) - Method in class relations.ChunkAnalyzer: print chunks contain marker word
printChunk(List<Chunk>) - Method in class relations.SenAnalyzer
printChunkList() - Method in class relations.EventExtraction
printCompoundEvent(int) - Method in class relations.Eval
printCompoundTrigger(TData, List<Word>) - Method in class relations.Eval
printEventbyType(int, String) - Method in class relations.Eval
printEvents(String) - Method in class relations.Eval
printEventType(int) - Method in class relations.Eval
printFile(String, String) - Method in class relations.Eval
printInChunks() - Method in class relations.SenAnalyzer
printInfo() - Method in class relations.Rules
processSentence(String, String[], int) - Method in class relations.SenAnalyzer
proCount() - Method in class relations.BasicChunk
proIDMap - Variable in class relations.SenAnalyzer
proMap - Variable in class relations.Eval
pros - Variable in class relations.Chunk
proWord - Variable in class relations.TriggerLearner

R

relations - package relations
relWords - Variable in class relations.TriggerLearner
removePRO(Word) - Method in class relations.Chunk
removePro(int) - Method in class relations.Chunk
removeTrg(Word) - Method in class relations.BasicChunk
removeTRG(Word) - Method in class relations.Chunk
required - Variable in class relations.KeyData
rs - Variable in class utils.DBUtils
RuleData - Class in relations
RuleData() - Constructor for class relations.RuleData
RuleData(int, String, String, boolean, String, boolean, int, String) - Constructor for class relations.RuleData
RuleData(int, String, String, boolean, boolean, boolean, String, String, boolean, boolean, int, int, String) - Constructor for class relations.RuleData
RuleData(int, String, String, boolean, boolean, boolean, String, String, boolean, boolean, int, int, boolean, boolean, String, String) - Constructor for class relations.RuleData
RuleLearner - Class in relations
RuleLearner() - Constructor for class relations.RuleLearner
RuleLearner(DBUtils, DBUtils) - Constructor for class relations.RuleLearner
Rules - Class in relations
Rules(int, String) - Constructor for class relations.Rules
RuleSet - Class in relations
RuleSet() - Constructor for class relations.RuleSet
RuleSets - Class in relations: Dec 12, 2011
RuleSets() - Constructor for class relations.RuleSets: group0 : in-chunk -> PRO-TG | POS: NN/JJ group1 : in-chunk + cause/theme2: PRO-TG PRO/EVT |POS: NN/JJ group2 : TG prep PRO/EVT (theme) | POS: NN/JJ/VB (active) group3 : TG prep PRO/EVT prep PRO/EVT |POS: NN/JJ/VB group4 : PRO/EVT (theme) TG | POS: NN/VB (passive)(binding) group5 : PRO/EVT (theme) (prep) TG (prep) PRO/EVT (cause) | POS: NN/VB(passive) group6 : PRO/EVT (cause) (prep) TG (prep) PRO/EVT (theme) | POS: NN/VB(active) group7 : PRO - PRO - TG For NP chunk -> POS: NNx/JJ/VBx With NNx -> possible group: G0,G1,G2,G3,G4,G5,G6,G7 -->Reg: G0,G1,G2(has prep or dist=0),G3, can skip G4,G6 -->Binding:G0,G1,G2(has prep or dist=0),G3, can skip G4, no G6 -->Simple:G0, G2 With JJ -> Possible group: G0,G1,G2, skip the other group With VBx -> Possible group: G2,G4,G5,G6 -->Reg: G2, G3(by), G5 (by); can skip G4,G0,G1 For VP chunk -> POS:JJ/VBx Possible group (Reg event): G2,G6 (active); G4,G5 (passive) ; For binding, no distinction between passive and active For simple event: G2 and G4

S

saveAbstract(String, String) - Method in class corpora.DataSaver
saveEquiv(String, String, String) - Method in class corpora.DataSaver: Store modified values
saveEvent(String, String, String, String, String, String, String) - Method in class corpora.DataSaver
saveModify(String, String, String, String) - Method in class corpora.DataSaver: Store modified values
saveProtein(String, String, int, int, String) - Method in class corpora.DataSaver
saveTrigger(String, String, String, int, int, String) - Method in class corpora.DataSaver: Store trigger into Trigger table
score - Variable in class relations.KeyData
SenAnalyzer - Class in relations
SenAnalyzer(SenSimplifier) - Constructor for class relations.SenAnalyzer: For creating new dictionary only
SenAnalyzer(DBUtils, DBUtils) - Constructor for class relations.SenAnalyzer: Use given database
senid - Variable in class parser.Parser
SenSimplifier - Class in relations
SenSimplifier(DBUtils) - Constructor for class relations.SenSimplifier
SenSimplifier() - Constructor for class relations.SenSimplifier
SentenceSplitter - Class in utils
SentenceSplitter() - Constructor for class utils.SentenceSplitter
SentenceSplitter.BioSemSentence - Class in utils
SentenceSplitter.BioSemSentence(String, int, int) - Constructor for class utils.SentenceSplitter.BioSemSentence
SentenceSplitter.BioSemSentence() - Constructor for class utils.SentenceSplitter.BioSemSentence
set2String(Set<String>) - Method in class relations.KeyData: Convert a map into string separeted by commar.
setChildTrigger(String) - Method in class relations.RuleData
setDb(DBUtils) - Method in class relations.EventExtraction
setDB(DBUtils) - Method in class relations.SenAnalyzer: Set default database
setDB(DBUtils) - Method in class relations.SenSimplifier: Set default database
setModifier() - Method in class relations.SenSimplifier: These data learn form Modifier Learner; It would be nicer to automatically set these modifiers.
setModifiers(String[]) - Method in class relations.KeyData: Set modifers for this trigger
setParentTrigger(String) - Method in class relations.RuleData
setPID(String) - Method in class relations.PData
setSimpleDic(Set<String>) - Method in class relations.SenSimplifier
setToStr(Set<String>) - Method in class relations.RuleLearner
sharedDic - Variable in class relations.SenSimplifier
shutdownDB() - Method in class utils.DBUtils
simpleDic - Variable in class relations.SenSimplifier
skip - Variable in class relations.PData
skipMap - Variable in class relations.ChunkAnalyzer
skipPhrase(List<Chunk>, int, int) - Method in class relations.ChunkAnalyzer: First step: remove
splitData(List<TData>) - Method in class relations.Eval: Split list of Data (Trigger/Protein) based on number of sentences
splitData(List<TData>, int[]) - Method in class relations.SenAnalyzer: Split list of Data (Trigger/Protein) based on number of sentences
spliter(String) - Static method in class utils.SentenceSplitter
splitEvents(List<EData>) - Method in class relations.Eval: Spliting event per sentence
splitEvents(List<EData>) - Method in class relations.SenAnalyzer
splitTrg(List<Word>) - Method in class relations.Eval
splitTrg(List<Word>, int[]) - Method in class relations.SenAnalyzer
splitWord(String) - Method in class parser.Parser: Split text into tokens
stmt - Variable in class utils.DBUtils
storePatterns(Map<String, Rules>[], DBUtils) - Method in class relations.RuleLearner
storeRuleSet(Map<String, RuleSet>, DBUtils) - Method in class relations.RuleLearner

T

t2score - Variable in class relations.KeyData
TData - Class in relations
test() - Method in class relations.Eval
Test(String) - Method in class relations.EventExtraction
Test() - Method in class relations.EventExtraction
testAll() - Method in class relations.SenAnalyzer
testChunks() - Method in class relations.SenAnalyzer
testParser(String) - Method in class parser.Parser
testSentence() - Method in class relations.SenAnalyzer
testSpliter() - Method in class relations.SenSimplifier
text - Variable in class utils.SentenceSplitter.BioSemSentence
TID - Variable in class relations.Word
toString() - Method in class relations.BasicChunk: Operation: 1.
toString() - Method in class relations.Chunk
toString() - Method in class relations.EData
toString() - Method in class relations.PData
toString() - Method in class relations.Rules
toString() - Method in class relations.Word
total - Variable in class parser.Parser
trgCount() - Method in class relations.BasicChunk
trgIDMap - Variable in class relations.Eval
trig_ID - Variable in class relations.PData
trigger_type - Static variable in class relations.SenSimplifier
trigger_type - Static variable in class relations.TriggerLearner: Map between absolute position into related position of a given trigger with abstract/sentence
TriggerLearner - Class in relations
TriggerLearner(DBUtils, DBUtils) - Constructor for class relations.TriggerLearner
TriggerLearner.TriggerData - Class in relations
TriggerLearner.TriggerData(String, String) - Constructor for class relations.TriggerLearner.TriggerData
trigs - Variable in class relations.Chunk
trim(String) - Method in class relations.SenSimplifier
txt - Variable in class relations.Chunk
Txt2Db(String, String, boolean) - Method in class corpora.DataLoader
Txt2Db(String, String, List<String>) - Method in class corpora.DataLoader: Creates a database for event extraction as an programmatic API-call where all values are given directly rather then reading the values from files.
type - Variable in class relations.BasicChunk
type - Variable in class relations.Chunk
type - Variable in class relations.Word

U

used - Variable in class relations.Word
utils - package utils

V

VerbChunk - Class in relations
VerbChunk() - Constructor for class relations.VerbChunk

W

Word - Class in relations
Word(String, int, int) - Constructor for class relations.Word
word - Variable in class relations.Word
wordSpliter(String) - Static method in class utils.SentenceSplitter

A B C D E F G H I K L M N O P R S T U V W