title: Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.
abstract: The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Activity Flow language represents the influences of activities among various entities within a network. Unlike SBGN PD and ER that focus on the entities and their relationships with others, SBGN AF puts the emphasis on the functions (or activities) performed by the entities, and their effects to the functions of the same or other entities. The nodes (elements) describe the biological activities of the entities, such as protein kinase activity, binding activity or receptor activity, which can be easily mapped to Gene Ontology molecular function terms. The edges (connections) provide descriptions of relationships (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 biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.
authors.forename: Huaiyu
authors.initials: H
authors.lastname: Mi
authors.forename: Falk
authors.initials: F
authors.lastname: Schreiber
authors.forename: Stuart
authors.initials: S
authors.lastname: Moodie
authors.forename: Tobias
authors.initials: T
authors.lastname: Czauderna
authors.forename: Emek
authors.initials: E
authors.lastname: Demir
authors.forename: Robin
authors.initials: R
authors.lastname: Haw
authors.forename: Augustin
authors.initials: A
authors.lastname: Luna
authors.forename: Nicolas
authors.initials: N
authors.lastname: Le Novère
authors.forename: Anatoly
authors.initials: A
authors.lastname: Sorokin
authors.forename: Alice
authors.initials: A
authors.lastname: Villéger
mesh_terms: D000818:Animals; D064229:Biological Ontologies; D003196:Computer Graphics / Q000592:standards*; D066264:Datasets as Topic / Q000592:standards; D004282:Documentation / Q000592:standards; D006801:Humans; D016247:Information Storage and Retrieval / Q000592:standards; D038622:Internationality; D008954:Models, Biological; D011381:Programming Languages; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D049490:Systems Biology / Q000592:standards*
chemical_list: D020543:Proteome