PTM
assembly
mentions
PTMLUT
AssemblyExporter
PTMPrefixPat
ReachKBKeyTransforms
PaddingContext
context
PandasOutput
context
PaperId
PaperReader
PaperReader
reach
PathFinder
utils
PathwayUtils
fragmenter
PhosphorMutationPat
ReachKBKeyTransforms
PhysicalEntityUtils
fragmenter
Policy1
Engine
Policy2
Engine
Policy3
Engine
Policy4
Engine
PrecedenceRelation
assembly
PreprocessNxml
nxml
ProcessUtils
fragmenter
PropMap
JsonOutputter
ProteinDomainSuffixesFilename
ReachKBConstants
ProteinStopSuffixes
ReachKBConstants
padContext
BoundedPaddingContext
papersDir
RunAssembly
ReadPapers
parseAnnotation
Brat
parser
MyXML
participantOf
EntityUtils
pathwayComponentOf
ProcessUtils
pathwayComponents
PathwayUtils
polarity
Activation
ComplexEvent
Regulation
positive
AssemblyManager
precededBy
AssemblyExporter
Row
precedenceMentionLabel
SieveUtils
precedenceRelations
Event
predecessors
Event
predecessorsOf
AssemblyManager
preferSimpleEventControllers
DarpaActions
preferredLabel
MentionManager
preprocessedLatentStateMatrix
RuleBasedContextEngine
prettifyLabel
JsonOutputter
printCommands
ReachShell
proc
ReachShell
OpenSystem
NxmlSearcher
processPapers
ReachCLI
processor
ReachSystem
pronominalMatch
DarpaLinks
proteinBetween
DarpaActions
proteinDomainSuffixes
ReachKBKeyTransforms
proteinKeyTransforms
ReachKBKeyTransforms
proteinSearcher
EntityChecker
proteinSeq
ReachEntityLookup
pruneMentions
MentionFilter
publications
XReferrableUtils