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Canonical representation of BEL nodes and edges

This representation is incorporated into the "KAM visualization" style for the Cytoscape KAM Navigator plugin (https://github.com/OpenBEL/cytoscape-plugins)

Note: for any given BEL term, the node function refers to the outermost BEL function in the term. For example, both tscript(p(HGNC:JUN)) and tscript(complex(NCH:"AP-1 Complex")) will be colored as blue-purple hexagons based on the tscript() function, not the p() and complex() inner functions. At this time, no specific representation is provided for the abundance modification functions (pmod(), fus(), sub(), and trunc()), as they can only be used within an abundance function.

nodes

node function(s)Recommended Cytoscape shapesRecommended D3.js shapescolorwidth
proteinAbundance()rounded rectanglesquarecyan75
degradation()rounded rectanglesquareorange110
compositeAbundance()rounded rectanglesquarelight cyan150
complexAbundance()rounded rectanglesquaremedium blue150
rnaAbundance()ellipsecirclegreen75
microRNAAbundance()ellipsecirclegreen75
geneAbundance()ellipsecirclelight green75
pathology()parallelogramcrossorange125
biologicalProcess()parallelogramcrossmagenta125
reaction()parallelogramcrosslight purple150
abundance()diamondrhombuslight blue75
translocation()veetriangle-down

lavender

110
cellSecretion()veetriangle-downlavender110
cellSurfaceExpression()veetriangle-downlavender110
molecularActivity()hexagontriangle-upblue-purple110
gtpBoundActivity()hexagontriangle-upblue-purple110
catalyticActivity()hexagontriangle-upblue-purple110
chaperoneActivity()hexagontriangle-upblue-purple110
kinaseActivity()hexagontriangle-upblue-purple110
peptidaseActivity()hexagontriangle-upblue-purple110
phosphataseActivity()hexagontriangle-upblue-purple110
ribosylationActivity()hexagontriangle-upblue-purple110
transcriptionalActivity()hexagontriangle-upblue-purple110
transportActivity()hexagontriangle-upblue-purple110

edges

relationshipline stylewidthcolorsource arrowtarget arrow
decreasessolidlight (1.0)blacknonecircle
directlyDecreasessolidheavy (3.0)blacknonecircle
increasessolidlight (1.0)blacknonearrow
directlyIncreasessolidheavy (3.0)blacknonearrow

causesNoChange

backward slashheavy (3.0)blacknonehalf arrow bottom
negativeCorrelationdottedlight (1.0)blackcirclecircle
positiveCorrelationdottedlight (1.0)blackarrowarrow
associationdottedlight (1.0)blacknonenone
orthologousdashedheavy (3.0)graynonenone
transcribedTolong dashheavy (3.0)graynonediamond
translatedTolong dashheavy (3.0)graynonediamond
biomarkerFordottedlight (1.0)blacknonearrow
hasMemberdashedheavy (3.0)graynonediamond
hasComponentdashedheavy (3.0)graynonediamond
isAdashedheavy (3.0)graynonediamond
prognosticBiomarkerFordottedlight (1.0)blacknonearrow
rateLimitingStepOfdashedheavy (3.0)blacknonearrow
subProcessOfdashedheavy (3.0)graynonediamond
actsInlong dashheavy (3.0)graynonediamond
hasProductdashedheavy (3.0)graynonediamond
hasVariantdashedheavy (3.0)graynonediamond
hasModificationdashedheavy (3.0)graynonediamond
reactantIndashedheavy (3.0)graynonediamond
translocatesdashedheavy (3.0)graynonediamond
includesdashedheavy (3.0)graynonediamond

blue text - need to add to VizMapper file

orange text - change VizMapper file

 

 

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