The Systems Biology Graphical Notation

A group of scientists in the systems biology community propose visual conventions for drawing biological diagrams. 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 enab...

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Vydáno v:	Nature biotechnology Ročník 27; číslo 8; s. 735 - 741
Hlavní autoři:	Novère, Nicolas Le, Hucka, Michael, Mi, Huaiyu, Moodie, Stuart, Schreiber, Falk, Sorokin, Anatoly, Demir, Emek, Wegner, Katja, Aladjem, Mirit I, Wimalaratne, Sarala M, Bergman, Frank T, Gauges, Ralph, Ghazal, Peter, Kawaji, Hideya, Li, Lu, Matsuoka, Yukiko, Villéger, Alice, Boyd, Sarah E, Calzone, Laurence, Courtot, Melanie, Dogrusoz, Ugur, Freeman, Tom C, Funahashi, Akira, Ghosh, Samik, Jouraku, Akiya, Kim, Sohyoung, Kolpakov, Fedor, Luna, Augustin, Sahle, Sven, Schmidt, Esther, Watterson, Steven, Wu, Guanming, Goryanin, Igor, Kell, Douglas B, Sander, Chris, Sauro, Herbert, Snoep, Jacky L, Kohn, Kurt, Kitano, Hiroaki
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	New York Nature Publishing Group US 01.08.2009 Nature Publishing Group
Témata:	Agriculture Biochemistry Bioinformatics Biomedical and Life Sciences Biomedical Engineering/Biotechnology Biomedical research Biomedicine Biotechnology Chemistry Computer Graphics - history History, 20th Century Information management Internet Life Sciences Notation perspective Scientists Software Symbols Systems biology Systems Biology - history Visual programming (Computer science) Visual programming languages (Computer science)
ISSN:	1087-0156, 1546-1696, 1546-1696
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Abstract	A group of scientists in the systems biology community propose visual conventions for drawing biological diagrams. 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.
AbstractList	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. [PUBLICATION ABSTRACT] 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. 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.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. A group of scientists in the systems biology community propose visual conventions for drawing biological diagrams. 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.
Audience	Academic
Author	Demir, Emek Ghosh, Samik Moodie, Stuart Bergman, Frank T Sander, Chris Matsuoka, Yukiko Wu, Guanming Funahashi, Akira Sahle, Sven Watterson, Steven Snoep, Jacky L Sorokin, Anatoly Schmidt, Esther Wegner, Katja Dogrusoz, Ugur Freeman, Tom C Kohn, Kurt Kitano, Hiroaki Villéger, Alice Kell, Douglas B Schreiber, Falk Aladjem, Mirit I Kolpakov, Fedor Sauro, Herbert Ghazal, Peter Luna, Augustin Courtot, Melanie Novère, Nicolas Le Goryanin, Igor Wimalaratne, Sarala M Jouraku, Akiya Li, Lu Calzone, Laurence Kim, Sohyoung Gauges, Ralph Kawaji, Hideya Boyd, Sarah E Hucka, Michael Mi, Huaiyu
Author_xml	– sequence: 1 givenname: Nicolas Le surname: Novère fullname: Novère, Nicolas Le email: lenov@ebi.ac.uk organization: EMBL European Bioinformatics Institute – sequence: 2 givenname: Michael surname: Hucka fullname: Hucka, Michael organization: Engineering and Applied Science, California Institute of Technology – sequence: 3 givenname: Huaiyu surname: Mi fullname: Mi, Huaiyu organization: SRI International – sequence: 4 givenname: Stuart surname: Moodie fullname: Moodie, Stuart organization: Centre for Systems Biology at Edinburgh, University of Edinburgh – sequence: 5 givenname: Falk surname: Schreiber fullname: Schreiber, Falk organization: Leibniz Institute of Plant Genetics and Crop Plant Research, Institute of Computer Science, University of Halle – sequence: 6 givenname: Anatoly surname: Sorokin fullname: Sorokin, Anatoly organization: School of Informatics, University of Edinburgh – sequence: 7 givenname: Emek surname: Demir fullname: Demir, Emek organization: Memorial Sloan Kettering Cancer Center - Computational Biology Center – sequence: 8 givenname: Katja surname: Wegner fullname: Wegner, Katja organization: Science and Technology Research Institute, University of Hertfordshire – sequence: 9 givenname: Mirit I surname: Aladjem fullname: Aladjem, Mirit I organization: National Cancer Institute – sequence: 10 givenname: Sarala M surname: Wimalaratne fullname: Wimalaratne, Sarala M organization: Auckland Bioengineering Institute, University of Auckland – sequence: 11 givenname: Frank T surname: Bergman fullname: Bergman, Frank T organization: Department of Bioengineering, University of Washington – sequence: 12 givenname: Ralph surname: Gauges fullname: Gauges, Ralph organization: BIOQUANT, University of Heidelberg – sequence: 13 givenname: Peter surname: Ghazal fullname: Ghazal, Peter organization: Centre for Systems Biology at Edinburgh, University of Edinburgh, Division of Pathway Medicine, University of Edinburgh Medical School – sequence: 14 givenname: Hideya surname: Kawaji fullname: Kawaji, Hideya organization: Riken OMICS Science Center – sequence: 15 givenname: Lu surname: Li fullname: Li, Lu organization: EMBL European Bioinformatics Institute – sequence: 16 givenname: Yukiko surname: Matsuoka fullname: Matsuoka, Yukiko organization: The Systems Biology Institute – sequence: 17 givenname: Alice surname: Villéger fullname: Villéger, Alice organization: School of Computer Science, University of Manchester, Manchester Interdisciplinary Biocentre – sequence: 18 givenname: Sarah E surname: Boyd fullname: Boyd, Sarah E organization: Clayton School of Information Technology, Faculty of Information Technology, Monash University – sequence: 19 givenname: Laurence surname: Calzone fullname: Calzone, Laurence organization: U900 INSERM, Paris Mines Tech, Institut Curie – sequence: 20 givenname: Melanie surname: Courtot fullname: Courtot, Melanie organization: Terry Fox Laboratory, British Columbia Cancer Research Center – sequence: 21 givenname: Ugur surname: Dogrusoz fullname: Dogrusoz, Ugur organization: Bilkent Center for Bioinformatics, Bilkent University – sequence: 22 givenname: Tom C surname: Freeman fullname: Freeman, Tom C organization: Division of Pathway Medicine, University of Edinburgh Medical School, The Roslin Institute, University of Edinburgh – sequence: 23 givenname: Akira surname: Funahashi fullname: Funahashi, Akira organization: Department of Biosciences and Informatics, Keio University, Hiyoshi – sequence: 24 givenname: Samik surname: Ghosh fullname: Ghosh, Samik organization: The Systems Biology Institute – sequence: 25 givenname: Akiya surname: Jouraku fullname: Jouraku, Akiya organization: Department of Biosciences and Informatics, Keio University, Hiyoshi – sequence: 26 givenname: Sohyoung surname: Kim fullname: Kim, Sohyoung organization: National Cancer Institute – sequence: 27 givenname: Fedor surname: Kolpakov fullname: Kolpakov, Fedor organization: Institute of Systems Biology, Design Technological Institute of Digital Techniques SB RAS – sequence: 28 givenname: Augustin surname: Luna fullname: Luna, Augustin organization: National Cancer Institute – sequence: 29 givenname: Sven surname: Sahle fullname: Sahle, Sven organization: BIOQUANT, University of Heidelberg – sequence: 30 givenname: Esther surname: Schmidt fullname: Schmidt, Esther organization: EMBL European Bioinformatics Institute – sequence: 31 givenname: Steven surname: Watterson fullname: Watterson, Steven organization: Centre for Systems Biology at Edinburgh, University of Edinburgh, Bilkent Center for Bioinformatics, Bilkent University – sequence: 32 givenname: Guanming surname: Wu fullname: Wu, Guanming organization: Ontario Institute for Cancer Research – sequence: 33 givenname: Igor surname: Goryanin fullname: Goryanin, Igor organization: Centre for Systems Biology at Edinburgh, University of Edinburgh – sequence: 34 givenname: Douglas B surname: Kell fullname: Kell, Douglas B organization: Manchester Interdisciplinary Biocentre, School of Chemistry, University of Manchester – sequence: 35 givenname: Chris surname: Sander fullname: Sander, Chris organization: Memorial Sloan Kettering Cancer Center - Computational Biology Center – sequence: 36 givenname: Herbert surname: Sauro fullname: Sauro, Herbert organization: Department of Bioengineering, University of Washington – sequence: 37 givenname: Jacky L surname: Snoep fullname: Snoep, Jacky L organization: Department of Biochemistry, Stellenbosch University – sequence: 38 givenname: Kurt surname: Kohn fullname: Kohn, Kurt organization: National Cancer Institute – sequence: 39 givenname: Hiroaki surname: Kitano fullname: Kitano, Hiroaki organization: The Systems Biology Institute, Sony Computer Science Laboratories, Okinawa Institute of Science and Technology
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/19668183$$D View this record in MEDLINE/PubMed
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Snippet	A group of scientists in the systems biology community propose visual conventions for drawing biological diagrams. Circuit diagrams and Unified Modeling... Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity,...
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SubjectTerms	Agriculture Biochemistry Bioinformatics Biomedical and Life Sciences Biomedical Engineering/Biotechnology Biomedical research Biomedicine Biotechnology Chemistry Computer Graphics - history History, 20th Century Information management Internet Life Sciences Notation perspective Scientists Software Symbols Systems biology Systems Biology - history Visual programming (Computer science) Visual programming languages (Computer science)
Title	The Systems Biology Graphical Notation
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