TY - JOUR
T1 - The Systems Biology Markup Language (SBML)
T2 - Language Specification for Level 3 Version 2 Core
AU - Hucka, Michael
AU - Bergmann, Frank T.
AU - Dräger, Andreas
AU - Hoops, Stefan
AU - Keating, Sarah M.
AU - Le Novère, Nicolas
AU - Myers, Chris J.
AU - Olivier, Brett G.
AU - Sahle, Sven
AU - Schaff, James C.
AU - Smith, Lucian P.
AU - Waltemath, Dagmar
AU - Wilkinson, Darren J.
PY - 2018/6/19
Y1 - 2018/6/19
N2 - 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 Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.
AB - 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 Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.
KW - computational biology
KW - modeling
KW - SBML
KW - standards
KW - systems biology
UR - http://www.scopus.com/inward/record.url?scp=85055605401&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85055605401&partnerID=8YFLogxK
UR - https://www.mendeley.com/catalogue/28328781-9b6c-3d10-8740-565f7b762199/
U2 - 10.1515/jib-2017-0081
DO - 10.1515/jib-2017-0081
M3 - Article
C2 - 29522418
AN - SCOPUS:85055605401
SN - 1613-4516
VL - 15
SP - 1
EP - 182
JO - Journal of Integrative Bioinformatics
JF - Journal of Integrative Bioinformatics
IS - 1
ER -