Standard Formats

Displaying: 1 Found: 1 Total: 18


SBGN AF L1 V1.0


SBGN Activity Flow language Level 1 Version 1.0

Synopsis

AF depicts the influence between elements.

Description

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, specialized 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 ranging from textbooks and teaching in high schools to peer reviewed articles in scientific journals. The first level of the SBGN Activity Flow language has been publicly released. Shared by the communities of biochemists, genomic scientists, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signaling pathways, metabolic networks and gene regulatory maps.*

*(Mi, Huaiyu et al.. Available from Nature Precedings (2009))

Publication Date

09/2009

Authors

Moodie, Stuart
Le Novère, Nicolas
Mi, Huaiyu
Schreiber, Falk
Sorokin, Anatoly

Organizations


Biological Scales

Scale molecular cellular tissue organ organism ecosystem
Support unknown unknown unknown unknown unknown unknown

Spatial Representation

Spatial Representation Level Compartment Dimensions Gradients Spatial Structures
Support intrinsic unknown unknown unknown

Modeling Formalisms for this format

Software support for this format

Examples for this format


Advantage

  • Standardized graphical layout of a model

Modularity: no


Components Relation
Flat Network: no


Supported Math


Unit Support

Unit Required: no

Support: no support


Annotation Support

Miriram Support: no

identifiers.org Support: no

Description

Additional information on glyphs uses controlled vocabulary from SBO.


There are no transformations available!

LibSBGN


Programming language

C++

Links

API

LibSBGN


Systems Biology Graphical Notation (SBGN)


Description

Systems Biology Graphical Notation aims at representing networks of biochemical interactions in a standard and unambigious way.


Publication date

08/2008

Organizations

Links

Webpage

Publication

All formats for this class

Free and Open


Description

Not closely defiened license allowing for free use and open participation. The product is viewed as community effort.