Systems biology graphical notation : activity flow language Level 1 Version 1.2

Abstract

The Systems Biological Graphical Notation (SBGN) is an international community effortfor standardized graphical representations of biological pathways and networks. The goalof SBGN is to provide unambiguous pathway and network maps for readers with differentscientific backgrounds as well as to support efficient and accurate exchange of biologicalknowledge between different research communities, industry, and other players in systemsbiology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) andActivity Flow (AF), allow for the representation of different aspects of biological and bio-chemical systems at different levels of detail.The SBGN Activity Flow language represents the influences of activities among variousentities within a network. Unlike SBGN PD and ER that focus on the entities and theirrelationships with others, SBGN AF puts the emphasis on the functions (or activities) per-formed by the entities, and their effects to the functions of the same or other entities. Thenodes (elements) describe the biological activities of the entities, such as protein kinaseactivity, binding activity or receptor activity, which can be easily mapped to Gene Ontol-ogy molecular function terms. The edges (connections) provide descriptions of relation-ships (or influences) between the activities, e.g., positive influence and negative influence.Among all three languages of SBGN, AF is the closest to signaling pathways in biolog-ical literature and textbooks, but its well-defined semantics offer a superior precision inexpressing biological knowledge.