The Experts below are selected from a list of 210 Experts worldwide ranked by ideXlab platform
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
Nature Precedings, 2009Co-Authors: Stuart Moodie, Nicolas Le Novère, Anatoly Sorokin, Huaiyu Mi, 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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The Systems Biology Graphical Notation.
Nature biotechnology, 2009Co-Authors: Nicolas Le Novère, Stuart Moodie, Anatoly Sorokin, Peter Ghazal, Huaiyu Mi, Emek Demir, Falk Schreiber, Michael Hucka, Yukiko Matsuoka, Sarah E. Boyd, Katja Wegner, Laurence Calzone, Hideya Kawaji, Alice Villéger, Ralph Gauges, Frank T Bergman, Sarala M Wimalaratne, Mirit I Aladjem, Lu Li, Melanie CourtotAbstract:Circuit Diagrams and Unified Modeling Language Diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: Process Diagram, entity relationship Diagram and activity flow Diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.
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perspective The Systems Biology Graphical Notation
Perspective, 2009Co-Authors: Nicolas Le Novère, Stuart Moodie, Katja Wegner, Mirit I Aladjem, Anatoly Sorokin, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Sarala M WimalaratneAbstract:Circuit Diagrams and Unified Modeling Language Diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: Process Diagram, entity relationship Diagram and activity flow Diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling
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Systems Biology Graphical Notation: Process Diagram Level 1
Nature Precedings, 2008Co-Authors: Nicolas Le Novère, Stuart Moodie, Katja Wegner, Anatoly Sorokin, Yukiko Matsuoka, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Hiroaki KitanoAbstract: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.
Falk Schreiber - 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
Nature Precedings, 2009Co-Authors: Stuart Moodie, Nicolas Le Novère, Anatoly Sorokin, Huaiyu Mi, 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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The Systems Biology Graphical Notation.
Nature biotechnology, 2009Co-Authors: Nicolas Le Novère, Stuart Moodie, Anatoly Sorokin, Peter Ghazal, Huaiyu Mi, Emek Demir, Falk Schreiber, Michael Hucka, Yukiko Matsuoka, Sarah E. Boyd, Katja Wegner, Laurence Calzone, Hideya Kawaji, Alice Villéger, Ralph Gauges, Frank T Bergman, Sarala M Wimalaratne, Mirit I Aladjem, Lu Li, Melanie CourtotAbstract:Circuit Diagrams and Unified Modeling Language Diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: Process Diagram, entity relationship Diagram and activity flow Diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.
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perspective The Systems Biology Graphical Notation
Perspective, 2009Co-Authors: Nicolas Le Novère, Stuart Moodie, Katja Wegner, Mirit I Aladjem, Anatoly Sorokin, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Sarala M WimalaratneAbstract:Circuit Diagrams and Unified Modeling Language Diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: Process Diagram, entity relationship Diagram and activity flow Diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling
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Systems Biology Graphical Notation: Process Diagram Level 1
Nature Precedings, 2008Co-Authors: Nicolas Le Novère, Stuart Moodie, Katja Wegner, Anatoly Sorokin, Yukiko Matsuoka, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Hiroaki KitanoAbstract: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.
Stuart Moodie - 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
Nature Precedings, 2009Co-Authors: Stuart Moodie, Nicolas Le Novère, Anatoly Sorokin, Huaiyu Mi, 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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The Systems Biology Graphical Notation.
Nature biotechnology, 2009Co-Authors: Nicolas Le Novère, Stuart Moodie, Anatoly Sorokin, Peter Ghazal, Huaiyu Mi, Emek Demir, Falk Schreiber, Michael Hucka, Yukiko Matsuoka, Sarah E. Boyd, Katja Wegner, Laurence Calzone, Hideya Kawaji, Alice Villéger, Ralph Gauges, Frank T Bergman, Sarala M Wimalaratne, Mirit I Aladjem, Lu Li, Melanie CourtotAbstract:Circuit Diagrams and Unified Modeling Language Diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: Process Diagram, entity relationship Diagram and activity flow Diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.
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perspective The Systems Biology Graphical Notation
Perspective, 2009Co-Authors: Nicolas Le Novère, Stuart Moodie, Katja Wegner, Mirit I Aladjem, Anatoly Sorokin, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Sarala M WimalaratneAbstract:Circuit Diagrams and Unified Modeling Language Diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: Process Diagram, entity relationship Diagram and activity flow Diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling
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Systems Biology Graphical Notation: Process Diagram Level 1
Nature Precedings, 2008Co-Authors: Nicolas Le Novère, Stuart Moodie, Katja Wegner, Anatoly Sorokin, Yukiko Matsuoka, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Hiroaki KitanoAbstract: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.
Huaiyu Mi - 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
Nature Precedings, 2009Co-Authors: Stuart Moodie, Nicolas Le Novère, Anatoly Sorokin, Huaiyu Mi, 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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The Systems Biology Graphical Notation.
Nature biotechnology, 2009Co-Authors: Nicolas Le Novère, Stuart Moodie, Anatoly Sorokin, Peter Ghazal, Huaiyu Mi, Emek Demir, Falk Schreiber, Michael Hucka, Yukiko Matsuoka, Sarah E. Boyd, Katja Wegner, Laurence Calzone, Hideya Kawaji, Alice Villéger, Ralph Gauges, Frank T Bergman, Sarala M Wimalaratne, Mirit I Aladjem, Lu Li, Melanie CourtotAbstract:Circuit Diagrams and Unified Modeling Language Diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: Process Diagram, entity relationship Diagram and activity flow Diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.
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perspective The Systems Biology Graphical Notation
Perspective, 2009Co-Authors: Nicolas Le Novère, Stuart Moodie, Katja Wegner, Mirit I Aladjem, Anatoly Sorokin, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Sarala M WimalaratneAbstract:Circuit Diagrams and Unified Modeling Language Diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: Process Diagram, entity relationship Diagram and activity flow Diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling
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Systems Biology Graphical Notation: Process Diagram Level 1
Nature Precedings, 2008Co-Authors: Nicolas Le Novère, Stuart Moodie, Katja Wegner, Anatoly Sorokin, Yukiko Matsuoka, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Hiroaki KitanoAbstract: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: Process Description language Level 1
Nature Precedings, 2009Co-Authors: Stuart Moodie, Nicolas Le Novère, Anatoly Sorokin, Huaiyu Mi, 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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The Systems Biology Graphical Notation.
Nature biotechnology, 2009Co-Authors: Nicolas Le Novère, Stuart Moodie, Anatoly Sorokin, Peter Ghazal, Huaiyu Mi, Emek Demir, Falk Schreiber, Michael Hucka, Yukiko Matsuoka, Sarah E. Boyd, Katja Wegner, Laurence Calzone, Hideya Kawaji, Alice Villéger, Ralph Gauges, Frank T Bergman, Sarala M Wimalaratne, Mirit I Aladjem, Lu Li, Melanie CourtotAbstract:Circuit Diagrams and Unified Modeling Language Diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: Process Diagram, entity relationship Diagram and activity flow Diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling.
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perspective The Systems Biology Graphical Notation
Perspective, 2009Co-Authors: Nicolas Le Novère, Stuart Moodie, Katja Wegner, Mirit I Aladjem, Anatoly Sorokin, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Sarala M WimalaratneAbstract:Circuit Diagrams and Unified Modeling Language Diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software tool support for communication of complex information. Ironically, despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: Process Diagram, entity relationship Diagram and activity flow Diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling
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Systems Biology Graphical Notation: Process Diagram Level 1
Nature Precedings, 2008Co-Authors: Nicolas Le Novère, Stuart Moodie, Katja Wegner, Anatoly Sorokin, Yukiko Matsuoka, Michael Hucka, Falk Schreiber, Emek Demir, Huaiyu Mi, Hiroaki KitanoAbstract: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.