BEL_to_English.tsv

# This file defines the translations used to convert a subset of BEL syntax
# to English. Lines beginning with a '#' character are ignored.
#
# The format of this file is:
# <regular expression><tab><replacement>
#
# The <regular expression> values are used by Java 7's regular expression
# engine. Refer to your resident cryptographer for reference. ;)
#

# BEL language relationship: decreases
(?<SUB>.*) (decreases|-\|) (?<OBJ>.*)	${SUB} decreases ${OBJ}

# BEL language relationship; increases
(?<SUB>.*) (increases|->) (?<OBJ>.*)	${SUB} increases ${OBJ}

# BEL language relationship; causesNoChange
(?<SUB>.*) causesNoChange (?<OBJ>.*)	${SUB} causes no significant change of ${OBJ}

# BEL language relationship; directlyDecreases
(?<SUB>.*) (directlyDecreases|=\|) (?<OBJ>.*)	${SUB} decreases ${OBJ} through direct physical interaction

# BEL language relationship; directlyIncreases
(?<SUB>.*) (directlyIncreases|=>) (?<OBJ>.*)	${SUB} increases ${OBJ} through direct physical interaction

# BEL language relationship; negativeCorrelation
(?<SUB>.*) negativeCorrelation (?<OBJ>.*)	${SUB} and ${OBJ} are negatively correlated

# BEL language relationship; positiveCorrelation
(?<SUB>.*) positiveCorrelation (?<OBJ>.*)	${SUB} and ${OBJ} are positively correlated

# BEL language relationship; orthologous
(?<SUB>.*) orthologous (?<OBJ>.*)	${SUB} and ${OBJ} are orthologous

# BEL language relationship; transcribedTo
(?<SUB>.*) (transcribedTo|:>) (?<OBJ>.*)	${SUB} is transcribed to ${OBJ}

# BEL language relationship; translatedTo
(?<SUB>.*) (translatedTo|>>) (?<OBJ>.*)	${SUB} is translated to ${OBJ}

# BEL language relationship; association
(?<SUB>.*) (association|--) (?<OBJ>.*)	${SUB} and ${OBJ} are associated

# BEL language relationship; biomarkerFor
(?<SUB>.*) biomarkerFor (?<OBJ>.*)	${SUB} is a biomarker for ${OBJ}

# BEL language relationship; hasMember
(?<SUB>.*) hasMember (?<OBJ>.*)	${SUB} has the member ${OBJ}

# BEL language relationship; hasMembers
(?<SUB>.*) hasMembers (?<OBJ>.*)	${SUB} has the members ${OBJ}

# BEL language relationship; hasComponent
(?<SUB>.*) hasComponent (?<OBJ>.*)	${SUB} has the component ${OBJ}

# BEL language relationship; hasComponents
(?<SUB>.*) hasComponents (?<OBJ>.*)	${SUB} has the components ${OBJ}

# BEL language relationship; isA
(?<SUB>.*) isA (?<OBJ>.*)	${SUB} is a ${OBJ}

# BEL language relationship; prognosticBiomarkerFor
(?<SUB>.*) prognosticBiomarkerFor (?<OBJ>.*)	${SUB} is a prognostic biomarker for ${OBJ}

# BEL language relationship; rateLimitingStepOf
(?<SUB>.*) rateLimitingStepOf (?<OBJ>.*)	${SUB} is a rate-limiting step of ${OBJ}

# BEL language relationship; subprocess
(?<SUB>.*) subProcessOf (?<OBJ>.*)	${SUB} is a subprocess of ${OBJ}

# BEL language function; proteinAbundance w/ proteinModification
^(?<OUTERFX>(p|proteinAbundance))\((?<NS>.*):(?<VAL>.*),( )*(?<INNERFX>(pmod|proteinModification))\((?<TYPE>\w+),( )*(?<AA>\w+),( )*(?<POS>\w+)\)\)(?<SP>( )+)	 the abundance of ${VAL} protein modified by ${TYPE} at ${AA} ${POS}${SP}
(?<SP>( )*)(?<OUTERFX>(p|proteinAbundance))\((?<NS>.*):(?<VAL>.*),( )*(?<INNERFX>(pmod|proteinModification))\((?<TYPE>\w+),( )*(?<AA>\w+),( )*(?<POS>\w+)\)\)	${SP}the abundance of ${VAL} protein modified by ${TYPE} at ${AA} ${POS}
^(?<OUTERFX>(p|proteinAbundance))\((?<NS>.*):(?<VAL>.*),( )*(?<INNERFX>(pmod|proteinModification))\((?<TYPE>\w+),( )*(?<AA>\w+)\)\)(?<SP>( )+)	the abundance of ${VAL} protein modified by ${TYPE} at ${AA}${SP}
(?<SP>( )*)(?<OUTERFX>(p|proteinAbundance))\((?<NS>.*):(?<VAL>.*),( )*(?<INNERFX>(pmod|proteinModification))\((?<TYPE>\w+),( )*(?<AA>\w+)\)\)	${SP}the abundance of ${VAL} protein modified by ${TYPE} at ${AA}
^(?<OUTERFX>(p|proteinAbundance))\((?<NS>.*):(?<VAL>.*),( )*(?<INNERFX>(pmod|proteinModification))\((?<TYPE>\w+)\)\)(?<SP>( )+)	the abundance of ${VAL} protein modified by ${TYPE}${SP}
(?<SP>( )*)(?<OUTERFX>(p|proteinAbundance))\((?<NS>.*):(?<VAL>.*),( )*(?<INNERFX>(pmod|proteinModification))\((?<TYPE>\w+)\)\)	${SP}the abundance of ${VAL} protein modified by ${TYPE}

# BEL language function; proteinAbundance w/ substitution
^(?<OUTERFX>(p|proteinAbundance))\((?<NS>.*):(?<VAL>.*),( )*(?<INNERFX>(sub|substitution))\((?<AAREF>\w+),( )*(?<AAVAR>\w+),( )*(?<POS>\w+)\)\)(?<SP>( )+)	the abundance of ${VAL} protein in which ${AAREF} is substituted with ${AAVAR} at codon ${POS}${SP}
(?<SP>( )*)(?<OUTERFX>(p|proteinAbundance))\((?<NS>.*):(?<VAL>.*),( )*(?<INNERFX>(sub|substitution))\((?<AAREF>\w+),( )*(?<AAVAR>\w+),( )*(?<POS>\w+)\)\)	${SP}the abundance of ${VAL} protein in which ${AAREF} is substituted with ${AAVAR} at codon ${POS}

# BEL language function;
^(?<OUTERFX>(g|geneAbundance))\((?<NS>.*):(?<VAL>.*),( )*(?<INNERFX>(fus|fusion))\((?<AAREF>\w+),( )*(?<AAVAR>\w+),( )*(?<POS>\w+)\)\)(?<SP>( )+)	the abundance of ${VAL} protein in which ${AAREF} is substituted with ${AAVAR} at codon ${POS}${SP}
(?<SP>( )*)(?<OUTERFX>(g|geneAbundance))\((?<NS>.*):(?<VAL>.*),( )*(?<INNERFX>(fus|fusion))\((?<AAREF>\w+),( )*(?<AAVAR>\w+),( )*(?<POS>\w+)\)\)	${SP}the abundance of ${VAL} protein in which ${AAREF} is substituted with ${AAVAR} at codon ${POS}

# BEL language function; proteinAbundance w/ truncation
^(?<OUTERFX>(p|proteinAbundance))\((?<NS>.*):(?<VAL>.*),( )*(?<INNERFX>(trunc|truncation))\((?<POS>\w+)\)\)(?<SP>( )+)	the abundance of ${VAL} protein truncated at ${POS}${SP}
(?<SP>( )*)(?<OUTERFX>(p|proteinAbundance))\((?<NS>.*):(?<VAL>.*),( )*(?<INNERFX>(trunc|truncation))\((?<POS>\w+)\)\)	${SP}the abundance of ${VAL} protein truncated at ${POS}

# BEL language function; abundance
^(?<FX>(a|abundance))\((?<NS>.*)(:)(?<VAL>.*)\)(?<SP>( )+)	the abundance of ${VAL}${SP}
(?<SP>( )*)(?<FX>(a|abundance))\((?<NS>.*)(:)(?<VAL>.*)\)	${SP}the abundance of ${VAL}

# BEL language function; proteinAbundance
^(?<FX>(p|proteinAbundance))\((?<NS>\w*)(:)(?<VAL>\w*)\)(?<SP>( )+)	the abundance of ${VAL}${SP}
(?<SP>( )*)(?<FX>(p|proteinAbundance))\((?<NS>\w*)(:)(?<VAL>\w*)\)	${SP}the abundance of ${VAL}

# BEL language function; complexAbundance
^(?<FX>(complex|complexAbundance))\((?<NS>.*):(?<VAL>.*)\)(?<SP>( )+)	the complex of ${VAL}${SP}
(?<SP>( )*)(?<FX>(complex|complexAbundance))\((?<NS>.*):(?<VAL>.*)\)$	${SP}the complex of ${VAL}
^(?<FX>(complex|complexAbundance))\((?<ARGS>.*)\)(?<SP>( )+)	the complex of ${ARGS}${SP}
(?<SP>( )*)(?<FX>(complex|complexAbundance))\((?<ARGS>.*)\)	${SP}the complex of ${ARGS}

# BEL language function; compositebundance
^(?<FX>(composite|compositeAbundance))\((?<ARGS>.*)\)(?<SP>( )+)	${ARGS} together${SP}
(?<SP>( )*)(?<FX>(composite|compositeAbundance))\((?<ARGS>.*)\)	${SP}${ARGS} together

# BEL language function; geneAbundance
^(?<FX>(g|geneAbundance))\((?<NS>.*):(?<VAL>.*)\)(?<SP>( )+)	the abundance of ${VAL} gene${SP}
(?<SP>( )*)(?<FX>(g|geneAbundance))\((?<NS>.*):(?<VAL>.*)\)	${SP}the abundance of ${VAL} gene

# BEL language function; microRNAAbundance
^(?<FX>(m|microRNAAbundance))\((?<NS>.*):(?<VAL>.*)\)(?<SP>( )+)	the abundance of ${VAL} microRNA${SP}
(?<SP>( )*)(?<FX>(m|microRNAAbundance))\((?<NS>.*):(?<VAL>.*)\)	${SP}the abundance of ${VAL} microRNA

# BEL language function; rna
^(?<FX>(r|rnaAbundance))\((?<NS>.*):(?<VAL>.*)\)(?<SP>( )+)	the abundance of ${VAL} RNA${SP}
(?<SP>( )*)(?<FX>(r|rnaAbundance))\((?<NS>.*):(?<VAL>.*)\)	${SP}the abundance of ${VAL} RNA

# BEL language function; biologicalProcess
^(?<FX>(bp|biologicalProcess))\((?<NS>.*):(?<VAL>.*)\)(?<SP>( )+)	the biological process of ${VAL}${SP}
(?<SP>( )*)(?<FX>(bp|biologicalProcess))\((?<NS>.*):(?<VAL>.*)\)	${SP}the biological process of ${VAL}${SP}

# BEL language function; pathology
^(?<FX>(path|pathology))\((?<NS>.*):(?<VAL>.*)\)(?<SP>( )+)	the pathology of ${VAL}${SP}
(?<SP>( )*)(?<FX>(path|pathology))\((?<NS>.*):(?<VAL>.*)\)	${SP}the pathology of ${VAL}

# BEL language function; catalyticActivity
^(?<FX>(cat|catalyticActivity))\((?<ARGS>.*)\)(?<SP>( )+)	the catalytic activity of ${ARGS}${SP}
(?<SP>( )*)(?<FX>(cat|catalyticActivity))\((?<ARGS>.*)\)	${SP}the catalytic activity of ${ARGS}

# BEL language function; chaperoneActivity
^(?<FX>(chap|chaperoneActivity))\((?<ARGS>.*)\)(?<SP>( )+)	the chaperone activity of ${ARGS} namespace ${VAL}${SP}
(?<SP>( )*)(?<FX>(chap|chaperoneActivity))\((?<ARGS>.*)\)	${SP}the chaperone activity of ${ARGS} namespace ${VAL}

# BEL language function; gtpBoundActivity
^(?<FX>(gtp|gtpBoundActivity))\((?<ARGS>.*)\)(?<SP>( )+)	the GTP-bound activity of ${ARGS} namespace ${VAL}${SP}
(?<SP>( )*)(?<FX>(gtp|gtpBoundActivity))\((?<ARGS>.*)\)	${SP}the GTP-bound activity of ${ARGS} namespace ${VAL}

# BEL language function; kinaseActivity
^(?<FX>(kin|kinaseActivity))\((?<ARGS>.*)\)(?<SP>( )+)	the kinase activity of ${ARGS}${SP}
(?<SP>( )*)(?<FX>(kin|kinaseActivity))\((?<ARGS>.*)\)	${SP}the kinase activity of ${ARGS}

# BEL language function; molecularActivity
^(?<FX>(act|molecularActivity))\((?<ARGS>.*)\)(?<SP>( )+)	the molecular activity of ${ARGS}${SP}
(?<SP>( )*)(?<FX>(act|molecularActivity))\((?<ARGS>.*)\)	${SP}the molecular activity of ${ARGS}

# BEL language function; peptidaseActivity
^(?<FX>(pep|peptidaseActivity))\((?<ARGS>.*)\)(?<SP>( )+)	the peptidase activity of ${ARGS}${SP}
(?<SP>( )*)(?<FX>(pep|peptidaseActivity))\((?<ARGS>.*)\)	${SP}the peptidase activity of ${ARGS}

# BEL language function; phosphataseActivity
^(?<FX>(phos|phosphataseActivity))\((?<ARGS>.*)\)(?<SP>( )+)	the phosphatase activity of ${ARGS}${SP}
(?<SP>( )*)(?<FX>(phos|phosphataseActivity))\((?<ARGS>.*)\)	${SP}the phosphatase activity of ${ARGS}

# BEL language function; ribosylationActivity
^(?<FX>(ribo|ribosylationActivity))\((?<ARGS>.*)\)(?<SP>( )+)	the ribosylation activity of ${ARGS}${SP}
(?<SP>( )*)(?<FX>(ribo|ribosylationActivity))\((?<ARGS>.*)\)	${SP}the ribosylation activity of ${ARGS}

# BEL language function; transcriptionalActivity
^(?<FX>(tscript|transcriptionalActivity))\((?<ARGS>.*)\)(?<SP>( )+)	the transcriptional activity of ${ARGS}${SP}
(?<SP>( )*)(?<FX>(tscript|transcriptionalActivity))\((?<ARGS>.*)\)	${SP}the transcriptional activity of ${ARGS}

# BEL language function; transportActivity
^(?<FX>(tport|transportActivity))\((?<ARGS>.*)\)(?<SP>( )+)	the transport activity of ${ARGS}${SP}
(?<SP>( )*)(?<FX>(tport|transportActivity))\((?<ARGS>.*)\)	${SP}the transport activity of ${ARGS}

# BEL language function; translocation
^(?<FX>(tloc|translocation))\((?<ARGS>.*),( )*(?<NS1>\w*):(?<VAL1>\w*),( )*(?<NS2>\w*):(?<VAL2>\w*)\)(?<SP>( )*)	the translocation of ${ARGS} from the ${NS1} namespace cellular location ${VAL1} to the ${NS2} namespace cellular location ${VAL2}${SP}
(?<SP>( )*)(?<FX>(tloc|translocation))\((?<ARGS>.*),( )*(?<NS1>\w*):(?<VAL1>\w*),( )*(?<NS2>\w*):(?<VAL2>\w*)\)	${SP}the translocation of ${ARGS} from the ${NS1} namespace cellular location ${VAL1} to the ${NS2} namespace cellular location ${VAL2}

# BEL language function; cellSecretion
^(?<FX>(sec|cellSecretion))\((?<ARGS>.*)\)(?<SP>( )+)	the secretion of ${ARGS}${SP}
(?<SP>( )*)(?<FX>(sec|cellSecretion))\((?<ARGS>.*)\)	${SP}the secretion of ${ARGS}

# BEL language function; cellSurfaceExpression
^(?<FX>(surf|cellSurfaceExpression))\((?<ARGS>.*)\)(?<SP>( )+)	the cell surface expression of ${ARGS}${SP}
(?<SP>( )*)(?<FX>(surf|cellSurfaceExpression))\((?<ARGS>.*)\)	${SP}the cell surface expression of ${ARGS}

# BEL language function; degradation
^(?<FX>(deg|degradation))\((?<ARGS>.*)\)(?<SP>( )+)	the degradation of ${ARGS}${SP}
(?<SP>( )*)(?<FX>(deg|degradation))\((?<ARGS>.*)\)	${SP}the degradation of ${ARGS}

# BEL language function; reaction
^(?<FX1>(rxn|reaction))\((?<FX2>(reactants))\((?<ARGS1>.*)\),( )*(?<FX3>(products))\((?<ARGS2>.*)\)\)(?<SP>( )*)	the reaction with reactants ${ARGS1} and products ${ARGS2}${SP}
(?<SP>( )*)(?<FX1>(rxn|reaction))\((?<FX2>(reactants))\((?<ARGS1>.*)\),( )*(?<FX3>(products))\((?<ARGS2>.*)\)\)	${SP}the reaction with reactants ${ARGS1} and products ${ARGS2}

# Improve modification and substitution functions
protein modified by P(?<SP> )?	protein modified by phosphorylation${SP}
protein modified by A(?<SP> )?	protein modified by acetylation${SP}
protein modified by F(?<SP> )?	protein modified by farnesylation${SP}
protein modified by G(?<SP> )?	protein modified by glycosylation${SP}
protein modified by H(?<SP> )?	protein modified by hydroxylation${SP}
protein modified by M(?<SP> )?	protein modified by methylation${SP}
protein modified by R(?<SP> )?	protein modified by ribosylation${SP}
protein modified by S(?<SP> )?	protein modified by sumoylation${SP}
protein modified by U(?<SP> )?	protein modified by ubiquitination${SP}
protein modified by (?<TYPE>(.)*) at A(?<SP> )?	protein modified by ${TYPE} at alanine${SP}
protein modified by (?<TYPE>(.)*) at R(?<SP> )?	protein modified by ${TYPE} at arginine${SP}
protein modified by (?<TYPE>(.)*) at N(?<SP> )?	protein modified by ${TYPE} at asparagine${SP}
protein modified by (?<TYPE>(.)*) at D(?<SP> )?	protein modified by ${TYPE} at aspartic acid${SP}
protein modified by (?<TYPE>(.)*) at C(?<SP> )?	protein modified by ${TYPE} at cysteine${SP}
protein modified by (?<TYPE>(.)*) at E(?<SP> )?	protein modified by ${TYPE} at glutamic acid${SP}
protein modified by (?<TYPE>(.)*) at Q(?<SP> )?	protein modified by ${TYPE} at glutamine${SP}
protein modified by (?<TYPE>(.)*) at G(?<SP> )?	protein modified by ${TYPE} at glycine${SP}
protein modified by (?<TYPE>(.)*) at H(?<SP> )?	protein modified by ${TYPE} at histidine${SP}
protein modified by (?<TYPE>(.)*) at I(?<SP> )?	protein modified by ${TYPE} at isoleucine${SP}
protein modified by (?<TYPE>(.)*) at L(?<SP> )?	protein modified by ${TYPE} at leucine${SP}
protein modified by (?<TYPE>(.)*) at K(?<SP> )?	protein modified by ${TYPE} at lysine${SP}
protein modified by (?<TYPE>(.)*) at M(?<SP> )?	protein modified by ${TYPE} at methionine${SP}
protein modified by (?<TYPE>(.)*) at F(?<SP> )?	protein modified by ${TYPE} at phenylalanine${SP}
protein modified by (?<TYPE>(.)*) at P(?<SP> )?	protein modified by ${TYPE} at proline${SP}
protein modified by (?<TYPE>(.)*) at S(?<SP> )?	protein modified by ${TYPE} at serine${SP}
protein modified by (?<TYPE>(.)*) at T(?<SP> )?	protein modified by ${TYPE} at threonine${SP}
protein modified by (?<TYPE>(.)*) at W(?<SP> )?	protein modified by ${TYPE} at tryptophan${SP}
protein modified by (?<TYPE>(.)*) at Y(?<SP> )?	protein modified by ${TYPE} at tyrosine${SP}
protein modified by (?<TYPE>(.)*) at V(?<SP> )?	protein modified by ${TYPE} at valine${SP}