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

Huaiyu Mi, Falk Schreiber, Stuart Moodie, Tobias Czauderna, Emek Demir, Robin Haw, Augustin Luna, Nicolas Le Novère, Anatoly Sorokin, Alice Villéger

    Research output: Contribution to journalArticleResearchpeer-review

    10 Citations (Scopus)

    Abstract

    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.

    Original languageEnglish
    Article number265
    Pages (from-to)340-381
    Number of pages42
    JournalJournal of integrative bioinformatics
    Volume12
    Issue number2
    DOIs
    Publication statusPublished - 2015

    Cite this

    Mi, Huaiyu ; Schreiber, Falk ; Moodie, Stuart ; Czauderna, Tobias ; Demir, Emek ; Haw, Robin ; Luna, Augustin ; Le Novère, Nicolas ; Sorokin, Anatoly ; Villéger, Alice. / Systems Biology Graphical Notation : Activity Flow language Level 1 Version 1.2. In: Journal of integrative bioinformatics. 2015 ; Vol. 12, No. 2. pp. 340-381.
    @article{3f08e5e2b0894852a7b47f6601013b09,
    title = "Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2",
    abstract = "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.",
    author = "Huaiyu Mi and Falk Schreiber and Stuart Moodie and Tobias Czauderna and Emek Demir and Robin Haw and Augustin Luna and {Le Nov{\`e}re}, Nicolas and Anatoly Sorokin and Alice Vill{\'e}ger",
    year = "2015",
    doi = "10.2390/biecoll-jib-2015-265",
    language = "English",
    volume = "12",
    pages = "340--381",
    journal = "Journal of integrative bioinformatics",
    issn = "1613-4516",
    publisher = "Walter de Gruyter",
    number = "2",

    }

    Mi, H, Schreiber, F, Moodie, S, Czauderna, T, Demir, E, Haw, R, Luna, A, Le Novère, N, Sorokin, A & Villéger, A 2015, 'Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2', Journal of integrative bioinformatics, vol. 12, no. 2, 265, pp. 340-381. https://doi.org/10.2390/biecoll-jib-2015-265

    Systems Biology Graphical Notation : Activity Flow language Level 1 Version 1.2. / Mi, Huaiyu; Schreiber, Falk; Moodie, Stuart; Czauderna, Tobias; Demir, Emek; Haw, Robin; Luna, Augustin; Le Novère, Nicolas; Sorokin, Anatoly; Villéger, Alice.

    In: Journal of integrative bioinformatics, Vol. 12, No. 2, 265, 2015, p. 340-381.

    Research output: Contribution to journalArticleResearchpeer-review

    TY - JOUR

    T1 - Systems Biology Graphical Notation

    T2 - Activity Flow language Level 1 Version 1.2

    AU - Mi, Huaiyu

    AU - Schreiber, Falk

    AU - Moodie, Stuart

    AU - Czauderna, Tobias

    AU - Demir, Emek

    AU - Haw, Robin

    AU - Luna, Augustin

    AU - Le Novère, Nicolas

    AU - Sorokin, Anatoly

    AU - Villéger, Alice

    PY - 2015

    Y1 - 2015

    N2 - 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.

    AB - 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.

    UR - http://www.scopus.com/inward/record.url?scp=84982094941&partnerID=8YFLogxK

    U2 - 10.2390/biecoll-jib-2015-265

    DO - 10.2390/biecoll-jib-2015-265

    M3 - Article

    C2 - 26528563

    AN - SCOPUS:84982094941

    VL - 12

    SP - 340

    EP - 381

    JO - Journal of integrative bioinformatics

    JF - Journal of integrative bioinformatics

    SN - 1613-4516

    IS - 2

    M1 - 265

    ER -