Systems Biology Graphical Notation : Activity Flow language Level 1 Version 1.2

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2015
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Mi, Huaiyu
Moodie, Stuart
Czauderna, Tobias
Demir, Emek
Haw, Robin
Luna, Augustin
Le Novère, Nicolas
Sorokin, Anatoly
Villéger, Alice
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Journal of integrative bioinformatics. 2015, 12(2), 265. eISSN 1613-4516. Verfügbar unter: doi: 10.2390/biecoll-jib-2015-265
Zusammenfassung

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.

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ISO 690MI, Huaiyu, Falk SCHREIBER, Stuart MOODIE, Tobias CZAUDERNA, Emek DEMIR, Robin HAW, Augustin LUNA, Nicolas LE NOVÈRE, Anatoly SOROKIN, Alice VILLÉGER, 2015. Systems Biology Graphical Notation : Activity Flow language Level 1 Version 1.2. In: Journal of integrative bioinformatics. 2015, 12(2), 265. eISSN 1613-4516. Verfügbar unter: doi: 10.2390/biecoll-jib-2015-265
BibTex
@article{Mi2015-09-04Syste-38193,
  year={2015},
  doi={10.2390/biecoll-jib-2015-265},
  title={Systems Biology Graphical Notation : Activity Flow language Level 1 Version 1.2},
  number={2},
  volume={12},
  journal={Journal of integrative bioinformatics},
  author={Mi, Huaiyu and Schreiber, Falk and Moodie, Stuart and Czauderna, Tobias and Demir, Emek and Haw, Robin and Luna, Augustin and Le Novère, Nicolas and Sorokin, Anatoly and Villéger, Alice},
  note={Article Number: 265}
}
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