Systems biology graphical notation markup language (SBGNML) version 0.3

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buir.contributor.authorDoğrusöz, Uğur
dc.citation.issueNumber2-3en_US
dc.citation.volumeNumber17en_US
dc.contributor.authorLuna, A.en_US
dc.contributor.authorBergmann, F. T.en_US
dc.contributor.authorCzauderna, T.en_US
dc.contributor.authorDoğrusöz, Uğuren_US
dc.contributor.authorRougny, A.en_US
dc.contributor.authorDräger, A.en_US
dc.contributor.authorTouré, V.en_US
dc.contributor.authorMazein, A.en_US
dc.contributor.authorMazein, M. L.en_US
dc.date.accessioned2021-02-17T07:57:39Z
dc.date.available2021-02-17T07:57:39Z
dc.date.issued2020
dc.departmentDepartment of Computer Engineeringen_US
dc.description.abstractThis document defines Version 0.3 Markup Language (ML) support for the Systems Biology Graphical Notation (SBGN), a set of three complementary visual languages developed for biochemists, modelers, and computer scientists. SBGN aims at representing networks of biochemical interactions in a standard, unambiguous way to 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. SBGN is defined neutrally to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML, the eXtensible Markup Language. The notable changes from the previous version include the addition of attributes for better specify metadata about maps, as well as support for multiple maps, sub-maps, colors, and annotations. These changes enable a more efficient exchange of data to other commonly used systems biology formats (e. g., BioPAX and SBML) and between tools supporting SBGN (e. g., CellDesigner, Newt, Krayon, SBGN-ED, STON, cd2sbgnml, and MINERVA). More details on SBGN and related software are available at http://sbgn.org. With this effort, we hope to increase the adoption of SBGN in bioinformatics tools, ultimately enabling more researchers to visualize biological knowledge in a precise and unambiguous manner.en_US
dc.description.sponsorshipThe 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.en_US
dc.identifier.doi10.1515/jib-2020-0016en_US
dc.identifier.issn1613-4516
dc.identifier.urihttp://hdl.handle.net/11693/73769
dc.language.isoEnglishen_US
dc.publisherDe Gruyteren_US
dc.relation.isversionofhttps://dx.doi.org/10.1515/jib-2020-0016en_US
dc.source.titleJournal of integrative bioinformaticsen_US
dc.subjectBiological process diagramsen_US
dc.subjectNetwork biologyen_US
dc.subjectPathway diagramen_US
dc.subjectSBGNen_US
dc.subjectSystems biologyen_US
dc.subjectVisualizationen_US
dc.titleSystems biology graphical notation markup language (SBGNML) version 0.3en_US
dc.typeArticleen_US
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