The Experts below are selected from a list of 7593 Experts worldwide ranked by ideXlab platform
Falk Schreiber - One of the best experts on this subject based on the ideXlab platform.
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systems biology Graphical Notation entity relationship language level 1 version 2
Journal of Integrative Bioinformatics, 2015Co-Authors: Anatoly Sorokin, Stuart Moodie, Nicolas Le Novère, Emek Demir, Falk Schreiber, Tobias Czauderna, Augustin Luna, Robin Haw, Alice VillégerAbstract: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.
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systems biology Graphical Notation activity flow language level 1 version 1 2
Journal of Integrative Bioinformatics, 2015Co-Authors: Falk Schreiber, Stuart Moodie, Nicolas Le Novère, Emek Demir, Anatoly Sorokin, Tobias Czauderna, Augustin Luna, Robin Haw, Alice VillégerAbstract: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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translation of sbgn maps process description to activity flow
BMC Systems Biology, 2013Co-Authors: Falk Schreiber, Tobias Czauderna, Torsten VogtAbstract:Background The Systems Biology Graphical Notation (SBGN) provides standard Graphical languages for representing cellular processes, interactions, and biological networks. SBGN consists of three languages: Process Descriptions (PD), Entity Relationships (ER), and Activity Flows (AF). Maps in SBGN PD are often large, detailed, and complex, therefore there is a need for a simplified illustration.
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Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation
Nature Protocols, 2012Co-Authors: Astrid Junker, Tobias Czauderna, Hendrick Rohn, Christian Klukas, Anja Hartmann, Falk SchreiberAbstract:The Systems Biology Graphical Notation (SBGN) is an emerging standard for the uniform representation of biological processes and networks. By using examples from gene regulation and metabolism, this protocol shows the construction of SBGN maps by either manual drawing or automatic translation using the tool SBGN-ED. In addition, it discusses the enrichment of SBGN maps with different kinds of -omics data to bring numerical data into the context of these networks in order to facilitate the interpretation of experimental data. Finally, the export of such maps to public websites, including clickable images, supports the communication of results within the scientific community. With regard to the described functionalities, other tools partially overlap with SBGN-ED. However, currently, SBGN-ED is the only tool that combines all of these functions, including the representation in SBGN, data mapping and website export. This protocol aims to assist scientists with the step-by-step procedure, which altogether takes ∼90 min.
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sbgn ed working with the systems biology Graphical Notation
Nature Precedings, 2011Co-Authors: Tobias Czauderna, Falk SchreiberAbstract:The Systems Biology Graphical Notation - SBGN [1] provides a standard for the visual representation of biochemical and cellular processes. SBGN aims to improve information exchange and to support the collaborative creation of large maps based on individual modules. The language contains three views of biological processes covering different levels of detail:(1) Process Description (PD): this sublanguage provides a detailed presentation of the temporal dependencies of biological interactions in a network;(2) Entity Relationship (ER): this sublanguage displays the relationships in which a given entity can participate in a network; and(3) Activity Flow (AF): this sublanguage shows the flow of information between biological entities in an abstract way.SBGN aims to support a more efficient and accurate communication of biological knowledge between different research communities. However, to increase its usage, tools for editing, validating, layouting and translating SBGN maps are desirable.We present novel developments in SBGN-ED [2], a tool which allows the creation of all three types of SBGN maps from scratch or the editing of existing maps, the validation of these maps for syntactical and semantical correctness, the translation of networks from databases such as KEGG into SBGN and the export of SBGN maps into several file and image formats. SBGN-ED is based on the Vanted system [3] for the integration, analysis and visualisation of experimental data within biological networks and functional hierarchies. We furthermore present some applications based on SBGN-ED such as RIMAS [4].SBGN-ED is freely available from http://www.sbgn-ed.org. The web site contains also tutorials and example files.[1] N. Le Novere et al. (2009) The systems biology Graphical Notation. Nature Biotechnology, 27: 735–741.[2] B.H. Junker, C. Klukas and F. Schreiber (2006) VANTED: a system for advanced data analysis and visualization in the context of biological networks. BMC Bioinformatics, 7: 109.1–109.13.[3] T. Czauderna, C. Klukas and F. Schreiber (2010) Editing, validating, and translating of SBGN maps. Bioinformatics, 26(18): 2340-2341.[3] A. Junker, A. Hartmann, F. Schreiber, H. Baumlein (2010) An engineers view on regulation of seed development. Trends in Plant Science 15(6): 303-307.
Nicolas Le Novère - One of the best experts on this subject based on the ideXlab platform.
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systems biology Graphical Notation process description language level 1 version 1 3
Journal of Integrative Bioinformatics, 2015Co-Authors: Stuart L Moodie, Emek Demir, Nicolas Le Novère, Alice VillégerAbstract: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.
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systems biology Graphical Notation entity relationship language level 1 version 2
Journal of Integrative Bioinformatics, 2015Co-Authors: Anatoly Sorokin, Stuart Moodie, Nicolas Le Novère, Emek Demir, Falk Schreiber, Tobias Czauderna, Augustin Luna, Robin Haw, Alice VillégerAbstract: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.
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systems biology Graphical Notation activity flow language level 1 version 1 2
Journal of Integrative Bioinformatics, 2015Co-Authors: Falk Schreiber, Stuart Moodie, Nicolas Le Novère, Emek Demir, Anatoly Sorokin, Tobias Czauderna, Augustin Luna, Robin Haw, Alice VillégerAbstract: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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Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2)
Nature Precedings, 2011Co-Authors: Nicolas Le Novère, Stuart Moodie, Emek Demir, Alice VillégerAbstract: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 Descriptions, the Entity Relationships and the Activity Flows. 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 current document presents version 1.2 of the first level of the SBGN Entity Relationship language. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signaling pathways, metabolic networks and gene regulatory maps.
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Systems Biology Graphical Notation: Process Description language Level 1
Nature Precedings, 2009Co-Authors: Stuart Moodie, Huaiyu Mi, Nicolas Le Novère, Anatoly Sorokin, Falk SchreiberAbstract: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.
Anatoly Sorokin - One of the best experts on this subject based on the ideXlab platform.
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systems biology Graphical Notation entity relationship language level 1 version 2
Journal of Integrative Bioinformatics, 2015Co-Authors: Anatoly Sorokin, Stuart Moodie, Nicolas Le Novère, Emek Demir, Falk Schreiber, Tobias Czauderna, Augustin Luna, Robin Haw, Alice VillégerAbstract: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.
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systems biology Graphical Notation activity flow language level 1 version 1 2
Journal of Integrative Bioinformatics, 2015Co-Authors: Falk Schreiber, Stuart Moodie, Nicolas Le Novère, Emek Demir, Anatoly Sorokin, Tobias Czauderna, Augustin Luna, Robin Haw, Alice VillégerAbstract: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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Systems Biology Graphical Notation: Process Description language Level 1
Nature Precedings, 2009Co-Authors: Stuart Moodie, Huaiyu Mi, Nicolas Le Novère, Anatoly Sorokin, Falk SchreiberAbstract: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.
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Systems Biology Graphical Notation: Activity Flow language Level 1
Nature Precedings, 2009Co-Authors: Falk Schreiber, Stuart Moodie, Nicolas Le Novère, Anatoly SorokinAbstract: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, specialized 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 Descriptions, the Entity Relationships and the Activity Flows. 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 ranging from textbooks and teaching in high schools to peer reviewed articles in scientific journals. The first level of the SBGN Activity Flow language has been publicly released. Shared by the communities of biochemists, genomic scientists, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signaling pathways, metabolic networks and gene regulatory maps.
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Systems Biology Graphical Notation: Entity Relationship language Level 1
Nature Precedings, 2009Co-Authors: Nicolas Le Novère, Stuart Moodie, Anatoly Sorokin, Falk SchreiberAbstract: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 Descriptions, the Entity Relationships and the Activity Flows. 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 Entity Relationship language has been publicly released. 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.
Stuart Moodie - One of the best experts on this subject based on the ideXlab platform.
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systems biology Graphical Notation activity flow language level 1 version 1 2
Journal of Integrative Bioinformatics, 2015Co-Authors: Falk Schreiber, Stuart Moodie, Nicolas Le Novère, Emek Demir, Anatoly Sorokin, Tobias Czauderna, Augustin Luna, Robin Haw, Alice VillégerAbstract: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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systems biology Graphical Notation entity relationship language level 1 version 2
Journal of Integrative Bioinformatics, 2015Co-Authors: Anatoly Sorokin, Stuart Moodie, Nicolas Le Novère, Emek Demir, Falk Schreiber, Tobias Czauderna, Augustin Luna, Robin Haw, Alice VillégerAbstract: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.
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Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2)
Nature Precedings, 2011Co-Authors: Nicolas Le Novère, Stuart Moodie, Emek Demir, Alice VillégerAbstract: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 Descriptions, the Entity Relationships and the Activity Flows. 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 current document presents version 1.2 of the first level of the SBGN Entity Relationship language. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signaling pathways, metabolic networks and gene regulatory maps.
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Systems Biology Graphical Notation: Process Description language Level 1
Nature Precedings, 2009Co-Authors: Stuart Moodie, Huaiyu Mi, Nicolas Le Novère, Anatoly Sorokin, Falk SchreiberAbstract: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.
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Systems Biology Graphical Notation: Activity Flow language Level 1
Nature Precedings, 2009Co-Authors: Falk Schreiber, Stuart Moodie, Nicolas Le Novère, Anatoly SorokinAbstract: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, specialized 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 Descriptions, the Entity Relationships and the Activity Flows. 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 ranging from textbooks and teaching in high schools to peer reviewed articles in scientific journals. The first level of the SBGN Activity Flow language has been publicly released. Shared by the communities of biochemists, genomic scientists, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signaling pathways, metabolic networks and gene regulatory maps.
Tobias Czauderna - One of the best experts on this subject based on the ideXlab platform.
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systems biology Graphical Notation markup language sbgnml version 0 3
Journal of Integrative Bioinformatics, 2020Co-Authors: Frank Bergmann, Ugur Dogrusoz, Adrien Rougny, Vasundra Toure, Tobias Czauderna, Alexander Mazein, Andreas Drager, Michael L Blinov, Augustin LunaAbstract:The development of SBGN was mainly supported by a grant from the Japanese New Energy and Industrial Technol- 2 ogy Development Organization (NEDO, http://www.nedo.go.jp/). The Okinawa Institute of Science and Tech- 3 nology (OIST, http://www.oist.jp/), the AIST Computational Biology Research Center (AIST CBRC, http://www. 4 cbrc.jp/index.eng.html) the British Biotechnology and Biological Sciences Research Council (BBSRC, http:// 5 www.bbsrc.ac.uk/) through a Japan Partnering Award, the European Media Laboratory (EML Research gGmbH, 6 http://www.eml-r.org/), and the Beckman Institute at the California Institute of Technology (http://bnmc. 7 caltech.edu) provided additional support for SBGN workshops. Some help was supplied by the Japan Science 8 and Technology Agency (JST, http://www.jst.go.jp/) and the Genome Network Project of the Japanese Ministry 9 of Education, Sports, Culture, Science, and Technology (MEXT, http://www.mext.go.jp/) for the development of 10 the gene regulation network aspect of SBGN, and from the Engineering and Physical Sciences Research Council (EP- 11 SRC, http://www.epsrc.ac.uk) during the redaction of the specification. The German Ministry of Education and 12 Research (https://www.bmbf.de/) provided support for an SBGN workshop, the redaction of the specification, 13 and development of the SBGNML specification (de.NBI partner project “ModSim” (FKZ: 031L0104A)). Funding 14 from National Institute of General Medical Sciences (NIGMS) grant (P41 GM103504), National Human Genome Re- 15 search Institute (NHGRI) grant (U41 HG006623), and The Scientific and Technological Research Council of Turkey 16 grant (113E161) was additionally used for work on the specification. Funding from the US National Institutes of 17 Health (NIH, grant number 2R01GM070923-13) supported software development related to SBGN.
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systems biology Graphical Notation process description language level 1 version 2 0
Journal of Integrative Bioinformatics, 2019Co-Authors: Adrien Rougny, Ugur Dogrusoz, Stuart L Moodie, Vasundra Toure, Irina Balaur, Tobias Czauderna, Hanna Borlinghaus, Alexander MazeinAbstract: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).
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systems biology Graphical Notation entity relationship language level 1 version 2
Journal of Integrative Bioinformatics, 2015Co-Authors: Anatoly Sorokin, Stuart Moodie, Nicolas Le Novère, Emek Demir, Falk Schreiber, Tobias Czauderna, Augustin Luna, Robin Haw, Alice VillégerAbstract: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.
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systems biology Graphical Notation activity flow language level 1 version 1 2
Journal of Integrative Bioinformatics, 2015Co-Authors: Falk Schreiber, Stuart Moodie, Nicolas Le Novère, Emek Demir, Anatoly Sorokin, Tobias Czauderna, Augustin Luna, Robin Haw, Alice VillégerAbstract: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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translation of sbgn maps process description to activity flow
BMC Systems Biology, 2013Co-Authors: Falk Schreiber, Tobias Czauderna, Torsten VogtAbstract:Background The Systems Biology Graphical Notation (SBGN) provides standard Graphical languages for representing cellular processes, interactions, and biological networks. SBGN consists of three languages: Process Descriptions (PD), Entity Relationships (ER), and Activity Flows (AF). Maps in SBGN PD are often large, detailed, and complex, therefore there is a need for a simplified illustration.
