Entity Visual Shape
Physical Entities, such as proteins, small molecules, complexes, etc. Ellipse Shape
Interaction Entities, such as biochemical reactions, catalysis, etc. Square Shape
Edge Type Arrow Shape
Inhibition Black inhibition arrow type
Containment, e.g. a complex can contain one or more proteins. Black ciricle arrow type
All other edge types, e.g. activation, left, right, etc. Black arrow type
Labels for Physical Entities
All physical entities will be labeled as follows:
[NAME] [-CHEMICAL MODIFICATION ABBR] [(CELLULAR LOCATION ABBR)]
where [CHEMICAL MODIFICATION ABBR] and [CELLULAR LOCATION ABBR] are one of the abbreviations described below.
Examples:
MITF MITF
MITF Phosphorylated MITF-P
MITF Phosphorylated, in the cytoplasm MITF-P (CP)
Abbreviations for Chemical Modifications
acetylated A
glycosylated G
phosphorylated P
proteolytic cleavage PCS
sumoylated S
ubiquitinated U
[All others] No Abbreviation provided
Abbreviations for Cellular Locations
centrosome CE
cytoplasm CY
endoplasmic reticulum ER
endosome EN
extracellular matrix EM
golgi apparatus GA
mitochondrion MI
nucleus NU
plasma membrane PM
ribosome RI
[All others] No Abbreviation provided