REGULATION_EVENTS
ReachConstants
REMOVAL_EVENTS
ReachConstants
RLKBFactory
grounding
RUN_ID
JsonOutputter
ReachCLI
reach
ReachCSV
reach
ReachConstants
reach
ReachContextKBLister
grounding
ReachEntityLookup
grounding
ReachGrounder
grounding
ReachIMKBLookups
grounding
ReachIMKBMentionLookups
grounding
ReachKBConstants
grounding
ReachKBKeyTransforms
grounding
ReachKBUtils
grounding
ReachRLKBLookups
grounding
ReachResults
Api
ReachShell
reach
ReachSystem
reach
ReadPapers
reach
Regulation
representations
Relation
brat
Resolutions
grounding
Response
ApiRuler
ReverseLookupKB
grounding
ReverseSpeciesLookup
ReachRLKBLookups
Row
export
RuleBasedContextEngine
rulebased
RuleReader
reach
Ruler
apis
RulerResults
apis
Rules
RuleReader
RunAnnotationEval
assembly
RunAssembly
assembly
RunNxml2Fries
nxml
r
Performance Performance
rdfId
BioPAXElementUtils
reach
AssemblyShell sista ReachCSV ReachShell Api ApiRuler Ruler
reachAlternateKeys
ReachKBKeyTransforms
reachRules
Ruler
readAndCheckBioPax
EntityChecker
readFile
RuleReader brat FileReader
readGZFile
FileReader
readIds
NxmlSearcher
readLines
ReachKBUtils
readMapFile
NxmlIndexer
readNxml
NxmlReader NxmlIndexer
readPaper
PaperReader
readPapers
PaperReader
readResource
RuleReader
readStandOff
Brat
reader
AssemblyShell ReachShell Api ApiRuler NxmlSearcher BRI
referenceURI
ExternalKBAccessor IMKBMetaInfo
regexFromTriggers
Labeler
reichenbachPrecedence
PrecedenceSieves
relation
AssemblyAnnotation
relationLUT
IdTracker
relations
assembly
relationships
XReferrableUtils
reload
RuleReader
removeDummy
DarpaActions
removeEntriesContainingID
AssemblyManager
removeEntriesContainingIDofEER
AssemblyManager
removeEntriesContainingIDofMention
AssemblyManager
removeEntriesCorrespondingToIDs
AssemblyManager
removeExtension
FileReader
replaceArgsWithRole
FeatureExtractor
replaceEntitiesWithLabel
FeatureExtractor
reportError
AssemblyExporter
representations
assembly
requiresCoref
CorpusBuilder
res
CrossValidateAssemblyRelationClassifier
resolve
Coref ExternalKBAccessor AzFailsafeKBML IMKBFamilyLookup IMKBFamilyMentionLookup IMKBLookup IMKBMentionLookup IMKBOrganCellTypeLookup IMKBOrganCellTypeMentionLookup IMKBProteinLookup IMKBProteinMentionLookup KBLookup KBMentionLookup
resolveAlt
IMKBLookup IMKBMentionLookup KBAltLookup KBAltMentionLookup
resolveByASpecies
AzFailsafeKBML IMKBFamilyLookup IMKBFamilyMentionLookup IMKBLookup IMKBMentionLookup IMKBOrganCellTypeLookup IMKBOrganCellTypeMentionLookup IMKBProteinLookup IMKBProteinMentionLookup KBLookup KBMentionLookup
resolveByASpeciesAlt
IMKBLookup IMKBMentionLookup KBAltLookup KBAltMentionLookup
resolveBySpecies
AzFailsafeKBML IMKBFamilyLookup IMKBFamilyMentionLookup IMKBLookup IMKBMentionLookup IMKBOrganCellTypeLookup IMKBOrganCellTypeMentionLookup IMKBProteinLookup IMKBProteinMentionLookup KBLookup KBMentionLookup
resolveBySpeciesAlt
IMKBLookup IMKBMentionLookup KBAltLookup KBAltMentionLookup
resolveComplexEvents
Coref
resolveCoref
ReachSystem
resolveDisplay
ReachSystem
resolveDisplayForArguments
ReachSystem
resolveEvidence
AssemblyExporter
resolveHuman
AzFailsafeKBML IMKBFamilyLookup IMKBFamilyMentionLookup IMKBLookup IMKBMentionLookup IMKBOrganCellTypeLookup IMKBOrganCellTypeMentionLookup IMKBProteinLookup IMKBProteinMentionLookup KBLookup KBMentionLookup
resolveHumanAlt
IMKBLookup IMKBMentionLookup KBAltLookup KBAltMentionLookup
resolveNoSpecies
AzFailsafeKBML IMKBFamilyLookup IMKBFamilyMentionLookup IMKBLookup IMKBMentionLookup IMKBOrganCellTypeLookup IMKBOrganCellTypeMentionLookup IMKBProteinLookup IMKBProteinMentionLookup KBLookup KBMentionLookup
resolveNoSpeciesAlt
IMKBLookup IMKBMentionLookup KBAltLookup KBAltMentionLookup
resolveSimpleEvents
Coref
resolveTBMs
Coref
resource
Normalization
resourceID
ExternalKBAccessor
resourceId
IMKBMetaInfo
resourcesPath
RuleReader
results
CrossValidateAssemblyRelationClassifier
right
ConversionUtils
roots
MentionManager
rowsWithOutputIDProblems
AssemblyExporter
rowsWithPrecededByIDProblems
AssemblyExporter
rs
AssemblyRelationClassifier CorpusReader PaperReader
rule
Performance
ruleMap
RulerResults
rulebased
context
rules
RulerResults
runOnFriesEntry
Api
runOnFriesEntryToJava
Api
runOnNxml
Api
runOnNxmlToJava
Api
runOnText
Api
runOnTextToJava
Api
runOpen
Ruler
runReach
Ruler
running
AssemblyShell ReachShell