Abstract

Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Descriptions, the Entity Relationships and the Activity Flows. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Entity Relationship language has been publicly released. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps.

Highlights

  • The goal of the Systems Biology Graphical Notation (SBGN) is to standardize the graphical/visual representation of essential biochemical and cellular processes

  • A level of one of the SBGN languages represents a set of features deemed to fit together cohesively, constituting a usable set of functionality that the user community agrees is sufficient for a reasonable set of tasks and goals

  • This example will be re-used throughout the description of the graphical symbols used by SBGN Entity Relationship Level 1

Read more

Summary

Introduction

The previous chapters describe the appearance and meaning of SBGN Entity Relationship Level 1 components which are entity nodes as well as relationships. SBGN Entity Relationship maps should be recognizable by the glyphs used, and by the general style of the layout. We provide guidelines for the layout of Entity Relationships, divided into two categories: 1. We provide a list of additional suggestions which may help in producing aesthetically more pleasant layouts, possibly easier to understand. Those layout guidelines are independent of the method used to produce the map, and apply to both manually drawn maps as well as maps produced by an automatic layout algorithm. The meaning of a graph should be conserved upon scaling as far as possible

SBGN levels and versions
CHAPTER 1. INTRODUCTION
Note on typographical convention
Overview
Controlled vocabularies used in SBGN Entity Relationship Level 1
Entity material types
Entity conceptual types
Macromolecule covalent modifications
Miscellaneous terms
Entity nodes
Glyph: Entity
Glyph: Outcome
Glyph: And
Glyph: Or
Glyph: Not
Glyph: delay
Glyph: Perturbing agent
Statements
Glyph: Assignment
Glyph: Interaction
Glyph: Modulation
Glyph: Stimulation
Glyph: Inhibition
Glyph: Necessary stimulation
Glyph: Absolute inhibition
Glyph: Logic arc
Glyph: Annotation
Auxiliary units
Glyph: State variable
Concepts
Syntax
CHAPTER 3. GRAMMAR OF ENTITY RELATIONSHIPS
Logical Operators
Node-node overlaps
Multiple entities to represent the same concept
Annotation links
Main contributors
Comprehensive list of contributors
Financial support
Generics and instances

Talk to us

Join us for a 30 min session where you can share your feedback and ask us any queries you have

Schedule a call

Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.