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Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions

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Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions Michael Hucka (Chair) California Institute of Technology, USA Stefan Hoops Virginia Bioinformatics Institute, USA Sarah M. Keating California Institute of Technology, USA Nicolas Le Nov`ere EMBL European Bioinformatics Institute, UK Sven Sahle University of Heidelberg, Germany Darren J. Wilkinson Newcastle University, UK [email protected] SBML Level 2 Version 4 Release 1 22 December 2008 Corrections and other changes to this SBML language specification may appear over time. Notifications of new releases are broadcast on the mailing list [email protected] Nature Precedings : doi:10.1038/npre.2008.2715.1 Posted 24 Dec 2008 The latest release of the SBML Level 2 Version 4 specification is available at http://sbml.org/specifications/sbml-level-2/version-4/ This release of the specification is available at http://sbml.org/specifications/sbml-level-2/version-4/release-1/ The list of known issues in all releases of SBML Level 2 Version 4 is available at http://sbml.org/specifications/sbml-level-2/version-4/errata/ The XML Schema for SBML Level 2 Version 4 is available at http://sbml.org/xml-schemas/ Contents 1 Introduction 3 1.1 Developments, discussions, and notifications of updates ............................... 3 1.2 SBML Levels, Versions, and Releases ....................................... 3 1.3 Language features and backward compatibility ................................... 4 1.4 Document conventions ............................................... 5 2 Overview of SBML 9 3 Preliminary definitions and principles 11 3.1 Primitive data types ................................................ 11 3.2 Type SBase .................................................... 13 3.3 The id and name attributes on SBML components ................................. 18 3.4 Mathematical formulas in SBML Level 2 ....................................... 20 4 SBML components 30 4.1 The SBML container ................................................ 30 4.2 Model ....................................................... 31 4.3 Function definitions ................................................ 33 4.4 Unit definitions .................................................. 35 4.5 Compartment types ................................................ 42 4.6 Species types ................................................... 43 4.7 Compartments .................................................. 44 4.8 Species ...................................................... 48 4.9 Parameters .................................................... 52 4.10 Initial assignments ................................................. 54 4.11 Rules ....................................................... 57 4.12 Constraints .................................................... 61 4.13 Reactions ..................................................... 63 4.14 Events ...................................................... 77 5 The Systems Biology Ontology and the sboTerm attribute 84 5.1 Principles ..................................................... 84 5.2 Using SBO and sboTerm ............................................. 85 5.3 Relationships to the SBML annotation element .................................. 90 5.4 Discussion .................................................... 91 6 A standard format for the annotation element 92 6.1 Motivation ..................................................... 92 6.2 XML namespaces in the standard annotation .................................... 92 6.3 General syntax for the standard annotation ..................................... 93 6.4 Use of URIs .................................................... 94 6.5 Relation elements ................................................. 95 6.6 Model history ................................................... 96 6.7 Examples ..................................................... 97 7 Example models expressed in XML using SBML 103 7.1 A simple example application of SBML ....................................... 103 7.2 Example involving units .............................................. 104 7.3 Example of a discrete version of a simple dimerization reaction ........................... 106 7.4 Example involving assignment rules ........................................ 108 7.5 Example involving algebraic rules .......................................... 110 Nature Precedings : doi:10.1038/npre.2008.2715.1 Posted 24 Dec 2008 7.6 Example with combinations of boundaryCondition and constant values on Species with RateRule objects .... 112 7.7 Example of translation from a multi-compartmental model to ODEs .......................... 113 7.8 Example involving function definitions ........................................ 116 7.9 Example involving delay functions ......................................... 117 7.10 Example involving events ............................................. 118 7.11 Example involving two-dimensional compartments ................................. 120 8 Discussion 125 8.1 Future enhancements: SBML Level 3 and beyond .................................. 125 Acknowledgments 127 A XML Schema for SBML 128 B XML Schema for MathML subset 137 C Validation rules for SBML 141 D A method for assessing whether an SBML model is overdetermined 154 E Mathematical consequences of the fast attribute on Reaction 157 F Processing and validating SBase notes and Constraint message content 159 G Major changes between versions of SBML Level 2 and implications for backward compatibility 160 G.1 Between Version 2 and Version 1 .......................................... 160 G.2 Between Version 3 and Version 2 .......................................... 161 G.3 Between Version 4 and Version 3 .......................................... 162 References 164 2 1 1 Introduction 2 We present the Systems Biology Markup Language (SBML) Level 2 Version 4 Release 1, a model repre- 3 sentation format for systems biology. SBML is oriented towards describing systems of biochemical reactions 4 of the sort common in research on a number of topics, including cell signaling pathways, metabolic path- 5 ways, biochemical reactions, gene regulation, and many others. SBML is defined in a neutral fashion with 6 respect to programming languages and software encoding; however, it is primarily oriented towards allowing 7 models to be encoded using XML, the eXtensible Markup Language (Bosak and Bray, 1999; Bray et al., 8 2000). This document contains many examples of SBML models written in XML, as well as the text of an 9 XML Schema (Biron and Malhotra, 2000; Fallside, 2000; Thompson et al., 2000) that defines SBML Level 2 10 Version 4. A downloadable copy of the XML Schema and other related documents and software are also 11 available from the SBML project web site, http://sbml.org/. 12 The SBML project is not an attempt to define a universal language for representing quantitative models. The 13 rapidly evolving views of biological function, coupled with the vigorous rates at which new computational 14 techniques and individual tools are being developed today, are incompatible with a one-size-fits-all idea of a 15 universal language. A more realistic alternative is to acknowledge the diversity of approaches and methods 16 being explored by different software tool developers, and seek a common intermediate format—a lingua 17 franca—enabling communication of the most essential aspects of the models. 18 The definition of the model description language presented here does not specify how programs should 19 communicate or read/write SBML. We assume that for a simulation program to communicate a model 20 encoded in SBML, the program will have to translate its internal data structures to and from SBML, use a 21 suitable transmission medium and protocol, etc., but these issues are outside of the scope of this document. 22 1.1 Developments, discussions, and notifications of updates 23 SBML has been, and continues to be, developed in collaboration with an international community of re- 24 searchers and software developers. As in many projects, the primary mode of interaction between members 25 is electronic mail. Discussions about SBML take place on the mailing list [email protected]. The 26 mailing list archives and a web browser-based interface to the list are available at http://sbml.org/forums/. 27 A low-volume, broadcast-only mailing list is available where notifications of revisions to the SBML speci- 28 fication, notices of votes on SBML technical issues, and other critical matters are announced. This list 29 is [email protected] and anyone may subscribe to it freely. This list will never be used for 30 advertising and its membership list will never be disclosed. It is vitally important that all users of SBML 31 stay informed about new releases and other developments by subscribing to this list, even if they do not wish 32 to participate in discussions on the [email protected] list. Please visit the SBML project web site, 33 http://sbml.org/, for information about how to subscribe to [email protected] as well as for Nature Precedings : doi:10.1038/npre.2008.2715.1 Posted 24 Dec 2008 34 access to the list archives. 35 In Section 8.1, we attempt to acknowledge as many contributors to SBML’s development as we can, but as 36 SBML evolves, it becomes increasingly difficult to detail the individual contributions on a project that has 37 truly become an international community effort. 38 1.2 SBML Levels, Versions, and Releases 39 Major editions of SBML are termed
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