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Analyzing SBGN-AF Networks Using Normal Logic Programs: Chapter 9

Adrien Rougny 1, 2 Christine Froidevaux 2, 1 Yoshitaka Yamamoto 3 Katsumi Inoue 4
1 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
4 Inoue Laobratory
NII - National Institute of Informatics
Abstract : This chapter focuses on the systems biology graphical notation activity flow language (SBGN-AF). A large part of the signaling networks present in the biological literature are represented in a graphical form that is close to SBGN-AF. Moreover, an increasing number of databases store such networks represented in SBGN-AF or in graphical forms that can be easily translated into SBGN-AF. The SBGN-AF language contains a set of glyphs that represent biological objects and relations between these objects. SBGN-AF contains five groups of glyphs: activity nodes, auxiliary units, container nodes, modulation arcs and logical operators. Activity nodes, container nodes and logical operators are the nodes of the network; modulation arcs are the edges. The chapter gives succinctly the signification of each type of glyph. It defines a particular type of logic programs; the normal logic programs (NLPs), and gives the semantics of these programs that will be used.
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https://hal.archives-ouvertes.fr/hal-01110123
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Submitted on : Tuesday, January 27, 2015 - 3:31:28 PM
Last modification on : Thursday, July 8, 2021 - 3:49:58 AM

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Adrien Rougny, Christine Froidevaux, Yoshitaka Yamamoto, Katsumi Inoue. Analyzing SBGN-AF Networks Using Normal Logic Programs: Chapter 9. Logical Modeling of Biological Systems, Wiley, 2014, 978-1-84821-680-8. ⟨10.1002/9781119005223.ch9⟩. ⟨hal-01110123⟩

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