Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3

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 su...

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Vydané v:Journal of integrative bioinformatics Ročník 12; číslo 2; s. 213 - 280
Hlavní autori: Moodie, Stuart, Le Novère, Nicolas, Demir, Emek, Mi, Huaiyu, Villéger, Alice
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: Germany IMBio e.V 04.09.2015
Predmet:
Animals
Biological Ontologies
Computer Graphics - standards
Datasets as Topic - standards
Documentation - standards
Guidelines as Topic - standards
Humans
Information Storage and Retrieval - standards
Internationality
Models, Biological
Programming Languages
Proteome - metabolism
Signal Transduction - physiology
Systems Biology - standards
ISSN:1613-4516, 1613-4516
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Popis
Shrnutí: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 Process Description language represents biological entities and processes between these entities within a network. SBGN PD focuses on the mechanistic description and temporal dependencies of biological interactions and transformations. The nodes (elements) are split into entity nodes describing, e.g., metabolites, proteins, genes and complexes, and process nodes describing, e.g., reactions and associations. The edges (connections) provide descriptions of relationships (or influences) between the nodes, such as consumption, production, stimulation and inhibition. Among all three languages of SBGN, PD is the closest to metabolic and regulatory pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.
Bibliografia:ObjectType-Article-2
SourceType-Scholarly Journals-1
ObjectType-Instructional Material/Guideline-1
ObjectType-Feature-3
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ISSN:1613-4516
1613-4516
DOI:10.2390/biecoll-jib-2015-263