The semantics of an SBGN diagram does not depend on the relative position of the symbols, or on colors, patterns, shades, shapes and thickness of edges. Therefore, the upper and lower diagrams are identical as far as SBGN is concerned, and have to be interpreted exactly the same way. (a) Process diagrams, explicitly displaying the four forms of ERK, phosphorylated and nonphosphorylated on the tyrosine and the threonine, as well as the processes of phosphorylation by MEK and the inhibition of MEK by complexation with u0126. Note that the inhibition in this diagram emerges from the sequestration of MEK and is not explicitly represented. The phosphorylation sites are represented by variables, which in this example are labeled simply as 'Y' and 'T' (but in general could be anything desired by the diagram author), shown adorning the main symbols for ERK. (b) Entity relationship diagrams, showing ERK and the assignment of its phosphorylations (at the tyrosine and threonine residues), as well as the relationships between those and MEK and u0126. Note that ERK appears only once in this diagram; the different possible states are not explicitly depicted. (c) Activity flow diagrams depicting the activation of ERK by MEK and the inhibition of MEK by u0126. In this notation, only the relevant activities of u0126, MEK and ERK are represented, as well as abstract representations of the influences of activities upon each other, whereas the biochemical details are omitted.
The Systems Biology Graphical Notation by
Nicolas Le Novère, Michael Hucka, Huaiyu Mi, Stuart Moodie, Falk Schreiber, Anatoly Sorokin, Emek Demir, Katja Wegner, Mirit I Aladjem, Sarala M Wimalaratne, Frank T Bergman, Ralph Gauges, Peter Ghazal, Hideya Kawaji, Lu Li, Yukiko Matsuoka, Alice Villéger, Sarah E Boyd, Laurence Calzone, Melanie Courtot, Ugur Dogrusoz, Tom C Freeman, Akira Funahashi, Samik Ghosh, Akiya Jouraku, Sohyoung Kim, Fedor Kolpakov, Augustin Luna, Sven Sahle, Esther Schmidt, Steven Watterson, Guanming Wu, Igor Goryanin, Douglas B Kell, Chris Sander, Herbert Sauro, Jacky L Snoep, Kurt Kohn&Hiroaki Kitano
Nature Biotechnology 27, 735 - 741 (2009) Published online: 7 August 2009