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Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

Hucka, Michael and Bergmann, Frank T. and Chaouiya, Claudine and Dräger, Andreas and Hoops, Stefan and Keating, Sarah M. and König, Matthias and Le Novère, Nicolas and Myers, Chris J. and Olivier, Brett G. and Sahle, Sven and Schaff, James C. and Sheriff, Rahuman and Smith, Lucian P. and Waltemath, Dagmar and Wilkinson, Darren J. and Zhang, Fengkai (2019) Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. Journal of Integrative Bioinformatics, 16 (2). Art. No. 20190021. ISSN 1613-4516. https://resolver.caltech.edu/CaltechAUTHORS:20190624-083727440

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Abstract

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. Release 2 corrects some errors and clarifies some ambiguities discovered in Release 1. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project website at http://sbml.org/.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1515/jib-2019-0021DOIArticle
ORCID:
AuthorORCID
Hucka, Michael0000-0001-9105-5960
Bergmann, Frank T.0000-0001-5553-4702
Chaouiya, Claudine0000-0003-2350-0756
Dräger, Andreas0000-0002-1240-5553
Hoops, Stefan0000-0001-8503-8371
Keating, Sarah M.0000-0002-3356-3542
König, Matthias0000-0003-1725-179X
Le Novère, Nicolas0000-0002-6309-7327
Myers, Chris J.0000-0002-8762-8444
Olivier, Brett G.0000-0002-5293-5321
Schaff, James C.0000-0003-3286-7736
Sheriff, Rahuman0000-0003-0705-9809
Smith, Lucian P.0000-0001-7002-6386
Waltemath, Dagmar0000-0002-5886-5563
Wilkinson, Darren J.0000-0003-0736-802X
Zhang, Fengkai0000-0001-7112-9328
Additional Information:© 2019 Michael Hucka et al., published by Walter de Gruyter GmbH, Berlin/Boston. This work is licensed under the Creative Commons Attribution 4.0 Public License. Received: 2019-03-30; Accepted: 2019-05-20; Published Online: 2019-06-20. The development of SBML was originally funded by the Japan Science and Technology Agency (JST) under the ERATO Kitano Symbiotic Systems Project during the years 2000–2003. From 2003 to the present, funding for development of SBML and associated software such as libSBML and the SBML Test Suite has been provided chiefly by the National Institute of General Medical Sciences (USA) via grant numbers GM070923 and GM077671. Additional grant funding has in the past been provided by National Human Genome Research Institute (USA); the International Joint Research Program of NEDO (Japan); the JST ERATO-SORST Program (Japan); the Japanese Ministry of Agriculture; the Japanese Ministry of Education, Culture, Sports, Science and Technology; the BBSRC e-Science Initiative (UK); the DARPA IPTO Bio-Computation Program (USA); the Army Research Office’s Institute for Collaborative Biotechnologies (USA); and the Air Force Office of Scientific Research (USA). Additional support has been or continues to be provided by the following institutions, either directly for activities related to SBML or indirectly by supporting the work of present and past SBML Editors: the Beckman Institute at the California Institute of Technology (USA), EML Research gGmbH (Germany), the University of Heidelberg (Germany), the European Molecular Biology Laboratory’s European Bioinformatics Institute (UK), the Molecular Sciences Institute (USA), the University of Hertfordshire (UK), the University of Newcastle (UK), the Systems Biology Institute (Japan), and the Virginia Bioinformatics Institute (USA). Fengkai Zhang was supported by the intramural program of NIAID, NIH. The following individuals served as past SBML Editors and authors of SBML specifications. Their efforts helped shape what SBML is today: Hamid Bolouri; Andrew M. Finney; Herbert M. Sauro. SBML was first conceived at the JST/ERATO-sponsored First Workshop on Software Platforms for Systems Biology, held in April, 2000, at the California Institute of Technology in Pasadena, California, USA. The participants collectively decided to begin developing a common XML-based declarative language for representing models. The development and evolution of the Systems Biology Markup Language has continued ever since. Many discussions are archived online in the mailing list/forums area of http://sbml.org; many more discussions took place during meetings and workshops (a list of which is also available at http://sbml.org). SBML Level 3 has benefitted from so many contributions, large and small, by so many people who constitute the international SBML Forum, that we regret it has become infeasible to list individuals by name. We thank everyone who has participated in SBML’s development throughout the years, and we hope that this latest specification before you is a good step forward in SBML’s continued evolution.
Funders:
Funding AgencyGrant Number
Japan Science and Technology AgencyUNSPECIFIED
NIHGM070923
NIHGM077671
National Human Genome Research InstituteUNSPECIFIED
International Joint Research Program of NEDO (Japan)UNSPECIFIED
Ministry of Agriculture (Japan)UNSPECIFIED
Ministry of Education, Culture, Sports, Science and Technology (MEXT)UNSPECIFIED
Biotechnology and Biological Sciences Research Council (BBSRC)UNSPECIFIED
Defense Advanced Research Projects Agency (DARPA)UNSPECIFIED
Army Research Office (ARO)UNSPECIFIED
Air Force Office of Scientific Research (AFOSR)UNSPECIFIED
Caltech Beckman InstituteUNSPECIFIED
EML Research gGmbH (Germany)UNSPECIFIED
University of HeidelbergUNSPECIFIED
European Molecular Biology Laboratory (EMBL)UNSPECIFIED
Molecular Sciences InstituteUNSPECIFIED
University of HertfordshireUNSPECIFIED
University of NewcastleUNSPECIFIED
Systems Biology Institute (Japan)UNSPECIFIED
Virginia Bioinformatics InstituteUNSPECIFIED
Subject Keywords:Systems Biology Markup Language; Standards; Visualization; Representation
Issue or Number:2
Record Number:CaltechAUTHORS:20190624-083727440
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20190624-083727440
Official Citation:Hucka, M., Bergmann, F., Chaouiya, C., et al. (2019). The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. Journal of Integrative Bioinformatics, 16(2), pp. 20190021, doi: 10.1515/jib-2019-0021
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:96655
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:24 Jun 2019 17:05
Last Modified:03 Oct 2019 21:24

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