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  • 1
    Online Resource
    Online Resource
    Systems Biology Graphical Notation: Process Diagram Level 1
    Springer Science and Business Media LLC ; 2008
    In:  Nature Precedings
    Details
    In: Nature Precedings, Springer Science and Business Media LLC
    Abstract: 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, specialised 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 Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. 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 in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps.
    Type of Medium: Online Resource
    ISSN: 1756-0357
    URL: Article
    DOI: 10.1038/npre.2008.2320.1
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2008
    detail.hit.zdb_id: 2637018-9
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  • 2
    Online Resource
    Online Resource
    LibSBGN: Electronic Processing of SBGN maps
    Springer Science and Business Media LLC ; 2011
    In:  Nature Precedings ( 2011-9-8)
    Details
    In: Nature Precedings, Springer Science and Business Media LLC, ( 2011-9-8)
    Type of Medium: Online Resource
    ISSN: 1756-0357
    URL: Article
    DOI: 10.1038/npre.2010.4967
    Language: Unknown
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2011
    detail.hit.zdb_id: 2637018-9
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  • 3
    Online Resource
    Online Resource
    LibSBGN: Electronic Processing of SBGN maps
    Springer Science and Business Media LLC ; 2011
    In:  Nature Precedings
    Details
    In: Nature Precedings, Springer Science and Business Media LLC
    Abstract: Introduction Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that enables diagram exchange while preserving biological meaning and relations. Results To meet this need, we are developing an Extensible Markup Language (XML) schema definition. In addition we are developing a software library called LibSBGN. Besides reading and writing files, this library will also be used to validate SBGN maps against the specifications, and convert to and from related systems biology standards, such as SBML and BioPAX.LibSBGN is still under development, but is already being adopted by several tools (See the LibSBGN project page for an up-to-date list of client software). The early adoption of LibSBGN by those tools helps to ensure that LibSBGN is independent of a specific software application, and does not contain artifacts for specific tools. LibSBGN is currently implemented in Java, a parallel C++ version is planned for the future.A test-suite of dozens of LibSBGN documents, covering every possible feature of SBGN maps, was created. This test-suite can be used by developers to check for compliance with the standard, and compare rendering capabilities with other tools.LibSBGN is a community effort, involving people from institutes all around the world, representing a wide selection of pathway tools. The community is organized around a sourceforge project site (http://libsbgn.sourceforge.net), a mailing list and monthly online meetings.A first release of LibSBGN, covering only the Process Description (PD) language, is planned in October 2010. Support for all three languages of SBGN is planned for a later release.
    Type of Medium: Online Resource
    ISSN: 1756-0357
    URL: Article
    DOI: 10.1038/npre.2011.4967.2
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2011
    detail.hit.zdb_id: 2637018-9
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  • 4
    Online Resource
    Online Resource
    Software support for SBGN maps: SBGN-ML and LibSBGN
    Oxford University Press (OUP) ; 2012
    In:  Bioinformatics Vol. 28, No. 15 ( 2012-08-01), p. 2016-2021
    Details
    In: Bioinformatics, Oxford University Press (OUP), Vol. 28, No. 15 ( 2012-08-01), p. 2016-2021
    Abstract: Motivation: LibSBGN is a software library for reading, writing and manipulating Systems Biology Graphical Notation (SBGN) maps stored using the recently developed SBGN-ML file format. The library (available in C++ and Java) makes it easy for developers to add SBGN support to their tools, whereas the file format facilitates the exchange of maps between compatible software applications. The library also supports validation of maps, which simplifies the task of ensuring compliance with the detailed SBGN specifications. With this effort we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner. Availability and implementation: Milestone 2 was released in December 2011. Source code, example files and binaries are freely available under the terms of either the LGPL v2.1+ or Apache v2.0 open source licenses from http://libsbgn.sourceforge.net. Contact:  sbgn-libsbgn@lists.sourceforge.net
    Type of Medium: Online Resource
    ISSN: 1367-4811 , 1367-4803
    URL: Article
    DOI: 10.1093/bioinformatics/bts270
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2012
    detail.hit.zdb_id: 1468345-3
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    The Systems Biology Graphical Notation
    Springer Science and Business Media LLC ; 2009
    In:  Nature Biotechnology Vol. 27, No. 8 ( 2009-08), p. 735-741
    Details
    In: Nature Biotechnology, Springer Science and Business Media LLC, Vol. 27, No. 8 ( 2009-08), p. 735-741
    Type of Medium: Online Resource
    ISSN: 1087-0156 , 1546-1696
    URL: Article
    DOI: 10.1038/nbt.1558
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2009
    detail.hit.zdb_id: 1494943-X
    detail.hit.zdb_id: 1311932-1
    SSG: 12
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    Online Resource
  • 6
    Online Resource
    Online Resource
    LibSBGN: Electronic Processing of SBGN maps
    Springer Science and Business Media LLC ; 2010
    In:  Nature Precedings
    Details
    In: Nature Precedings, Springer Science and Business Media LLC
    Abstract: Introduction Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that enables diagram exchange while preserving biological meaning and relations. Results To meet this need, we are developing an Extensible Markup Language (XML) schema definition. In addition we are developing a software library called LibSBGN. Besides reading and writing files, this library will also be used to validate SBGN maps against the specifications, and convert to and from related systems biology standards, such as SBML and BioPAX.LibSBGN is still under development, but is already being adopted by several tools (See the LibSBGN project page for an up-to-date list of client software). The early adoption of LibSBGN by those tools helps to ensure that LibSBGN is independent of a specific software application, and does not contain artifacts for specific tools. LibSBGN is currently implemented in Java, a parallel C++ version is planned for the future.A test-suite of dozens of LibSBGN documents, covering every possible feature of SBGN maps, was created. This test-suite can be used by developers to check for compliance with the standard, and compare rendering capabilities with other tools.LibSBGN is a community effort, involving people from institutes all around the world, representing a wide selection of pathway tools. The community is organized around a sourceforge project site (http://libsbgn.sourceforge.net), a mailing list and monthly online meetings.A first release of LibSBGN, covering only the Process Description (PD) language, is planned in October 2010. Support for all three languages of SBGN is planned for a later release.
    Type of Medium: Online Resource
    ISSN: 1756-0357
    URL: Article
    DOI: 10.1038/npre.2010.4967.1
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2010
    detail.hit.zdb_id: 2637018-9
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  • 7
    Online Resource
    Online Resource
    Meeting report from the first meetings of the Computational Modeling in Biology Network (COMBINE)
    Springer Science and Business Media LLC ; 2011
    In:  Standards in Genomic Sciences Vol. 5, No. 2 ( 2011-11-30), p. 230-242
    Details
    In: Standards in Genomic Sciences, Springer Science and Business Media LLC, Vol. 5, No. 2 ( 2011-11-30), p. 230-242
    Type of Medium: Online Resource
    ISSN: 1944-3277
    URL: Article
    DOI: 10.4056/sigs.2034671
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2011
    detail.hit.zdb_id: 2586662-X
    detail.hit.zdb_id: 3007163-X
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  • 8
    Online Resource
    Online Resource
    Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2
    Walter de Gruyter GmbH ; 2015
    In:  Journal of Integrative Bioinformatics Vol. 12, No. 2 ( 2015-06-1), p. 281-339
    Details
    In: Journal of Integrative Bioinformatics, Walter de Gruyter GmbH, Vol. 12, No. 2 ( 2015-06-1), p. 281-339
    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 Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.
    Type of Medium: Online Resource
    ISSN: 1613-4516
    URL: Article
    DOI: 10.1515/jib-2015-264
    Language: Unknown
    Publisher: Walter de Gruyter GmbH
    Publication Date: 2015
    detail.hit.zdb_id: 2147212-9
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  • 9
    Online Resource
    Online Resource
    Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2
    Walter de Gruyter GmbH ; 2015
    In:  Journal of Integrative Bioinformatics Vol. 12, No. 2 ( 2015-06-1), p. 340-381
    Details
    In: Journal of Integrative Bioinformatics, Walter de Gruyter GmbH, Vol. 12, No. 2 ( 2015-06-1), p. 340-381
    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.
    Type of Medium: Online Resource
    ISSN: 1613-4516
    URL: Article
    DOI: 10.1515/jib-2015-265
    Language: Unknown
    Publisher: Walter de Gruyter GmbH
    Publication Date: 2015
    detail.hit.zdb_id: 2147212-9
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  • 10
    Online Resource
    Online Resource
    Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0
    Walter de Gruyter GmbH ; 2019
    In:  Journal of Integrative Bioinformatics Vol. 16, No. 2 ( 2019-06-13)
    Details
    In: Journal of Integrative Bioinformatics, Walter de Gruyter GmbH, Vol. 16, No. 2 ( 2019-06-13)
    Abstract: The Systems Biology Graphical Notation (SBGN) is an international community effort that aims to standardise the visualisation of pathways and networks for readers with diverse scientific backgrounds as well as to support an efficient and accurate exchange of biological knowledge between disparate research communities, industry, and other players in systems biology. SBGN comprises the three languages Entity Relationship, Activity Flow, and Process Description (PD) to cover biological and biochemical systems at distinct levels of detail. PD is closest to metabolic and regulatory pathways found in biological literature and textbooks. Its well-defined semantics offer a superior precision in expressing biological knowledge. PD represents mechanistic and temporal dependencies of biological interactions and transformations as a graph. Its different types of nodes include entity pools (e.g. metabolites, proteins, genes and complexes) and processes (e.g. reactions, associations and influences). The edges describe relationships between the nodes (e.g. consumption, production, stimulation and inhibition). This document details Level 1 Version 2.0 of the PD specification, including several improvements, in particular: 1) the addition of the equivalence operator, subunit, and annotation glyphs, 2) modification to the usage of submaps, and 3) updates to clarify the use of various glyphs (i.e. multimer, empty set, and state variable).
    Type of Medium: Online Resource
    ISSN: 1613-4516
    URL: Article
    DOI: 10.1515/jib-2019-0022
    Language: Unknown
    Publisher: Walter de Gruyter GmbH
    Publication Date: 2019
    detail.hit.zdb_id: 2147212-9
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