Overview
The Systems Biology Markup Language (SBML) is a computer-readable format for representing models of biological processes. It's applicable to simulations of metabolism, cell-signaling, and many other topics. SBML has been evolving since mid-2000 thanks to an international community of software developers and users...
"SBML is neutral with respect to programming languages and software encoding; however, it's oriented towards allowing models to be encoded using XML. By supporting SBML as a format for reading and writing models, different software tools (including programs for building and editing models, simulation programs, databases, and other systems) can directly communicate and store the same computable representation of those models. This removes an impediment to sharing results and permits other researchers to start with an unambiguous representation of the model, examine it carefully, propose precise corrections and extensions, and apply new techniques and approaches..."
Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene regulation etc., SBML can also be used to encode any kinetic model. SBML offers mechanisms to describe biological components by means of compartments and reacting species, as well as their dynamic behaviour, using reactions, events and arbitrary mathematical rules. SBML also offers all the housekeeping structures needed to ensure an unambiguous understanding of quantitative descriptions. Release 1 of the specification for SBML Level 2 Version 4 describes the structures of the language and the rules used to build a valid model. SBML XML Schema and other related documents and software are also available from the SBML project web site..."
[October 17, 2000] The Caltech ERATO Kitano Systems Biology Project is developing the Systems Biology Markup Language (SBML), using XML and UML for representation and modeling of the information components in the system. The research team is attempting to specify "a common, model-based description language for systems biology simulation software; we call this the Systems Biology Markup Language (SBML). The overall goal is to develop an open standard that will enable simulation software to communicate and exchange models, ultimately leading to the ability for researchers to run simulations and analyses across multiple software packages. SBML is the result of merging the most obvious modeling-language features of BioSpice, DBSolve, E-Cell, Gepasi, Jarnac, StochSim, and Virtual Cell. The description language is encoded in XML, the Extensible Markup Language. The XML encoding of the description language can define a file format; however, at this time, we are focusing on using the XML-based description language as an interchange format for use in communications between programs. Appendix B [in the principal specification] contains the current version of this XML schema. As XML Schemas are difficult to read and absorb by human readers, we define the proposed data structures using a succinct graphical notation based on a subset of UML, the Unified Modeling Language. . . The SBML representation language is organized around five categories of information: model, compartment, geometry, specie, and reaction. Not all ofthese will be needed by every simulation package; rather, the intent is to cover the range of data structures needed by the collection of all of the simulators examined so far..."
References:
"SCHUCS: A UML-Based Approach for Describing Data Representations Intended for XML Encoding." [cache]
A Notation for Describing Data Representations Intended for XML Encoding." September 9, 2000.
SBML XML Schema, 2000-10.
"An XML-Based Model Description Language for Systems Biology Simulations." By Andrew Finney, Herbert Sauro, Michael Hucka, and Hamid Bolouri. Email: {afinney,hsauro,mhucka,hbolouri}@cds.caltech.edu. ERATO Kitano Systems Biology Project [Control and Dynamical Systems 107-81]. California Institute of Technology, Pasadena,CA 91125. Version of September 12,2000. 27 pages. "We present a first attempt at specifying a common, model-based description language for systems biology simulation software. We call this this the Systems Biology Markup Language (SBML). The overall goal is to develop an open standard that will enable simulation software to communicate and exchange models, ultimately leading to the ability for researchers to run simulations and analyses across multiple software packages. SBML is the result of merging the most obvious modeling-language features of BioSpice, DBSolve, E-Cell, Gepasi, Jarnac, StochSim, and Virtual Cell. The description language is encoded in XML, the Extensible Markup Language. The XML encoding of the description language can define a file format; however, at this time, we are focusing on using the XML-based description language as an interchange format for use in communications between programs. The primary purpose of this document is to serve as a basis for discussion and further development of a more comprehensive language specification. The final outcome ofthis process will be an XML Schema which can be used to communicate model descriptions between simulation packages. Appendix B contains the current version of this XML schema. As XML Schemas are difficult to read and absorb by human readers, we define the proposed data structures using a succinct graphical notation based on a subset of UML, the Unified Modeling Language. Our notation is explained in "A Notation for Describing Data Representations Intended for XML Encoding" (Hucka,2000), available online at ftp://ftp.cds.caltech.edu/pub/caltech-erato/notation/. For the sake of clarity, we ask readers to use this notation when contributing to discussions about the specification. To facilitate discussions, a web/FTP site and a group mailing list have been set up for the participating groups. Please see the web site at http://www.cds.caltech.edu/erato/ for details. . . The representation language is organized around five categories of information: model, compartment, geometry, specie, and reaction. Not all ofthese will be needed by every simulation package; rather, the intent is to cover the range of data structures needed by the collection of all of the simulators examined so far. Appendix A contains several examples of models encoded in XML using SBML. We use portions of these models as illustrations throughout the rest of the document." [cache]
"A Notation for Describing Data Representations Intended for XML Encoding." By Michael Hucka (ERATO Kitano Systems Biology Project). Version of September 12, 2000. 15 pages. "One component of the ERATO Kitano Systems Biology Project is the creation of a workbench that provides interoperability between a number of simulation packages. Developing a framework for database storage and inter-program exchange requires defining a language for communicating data. Defining this language requires first establishing a notation that humans can use to describe the data structures involved. I propose a simple notation to be used for describing data structures that are intended to be encoded using XML, the Extensible Markup Language. The notation is based in part on a small subset of UML, the Unified Modeling Language, a visual language for specifying software systems. There are three main advantages to using UML class diagrams as a basis for defining data structures. First, compared to using other notations or a programming language, the UML visual representations are generally easier to read and understand by readers who are not computer scientists. Second,the visual notation is implementation- neutral -- the defined structures can be encoded in any concrete implementation language, not just XML but other formats as well, making the UML-based definitions more useful and flexible. Third, UML is a de facto industry standard, documented in many books and available in many software tools including mainstream development environments (such as Microsoft Visual Basic 5 Enterprise Edition). Readers are therefore more likely to be familiar with it than other notations. Readers do not need to know UML in advance; this document provides descriptions of all the constructs used. The notation presented here can be expressed not only in graphical diagram form (which is what UML is all about) but also in textual form, allowing descriptions to be easily written in a text editor and sent as plain text email. The scope of the notation is limited to classes and their attributes, not class methods or operations. One of the goals of this effort has been to develop a consistent, systematic method for translating UML-based class diagrams into XML Schemas.Another goal has been to maintain a reasonably simple notation and UML-to-XML mapping. An important side-effect of this is that the vocabulary of the notation is purposefully limited to only a handful of constructs. It is explicitly not intended to cover the full power of UML or XML. This limited vocabulary has nevertheless been sufficient for the applications to which it has been applied so far in the Systems Biology workbench project. The notation proposed in this document is based on a subset of what could be used and what UML provides. It is not intended to cover the full scope of UML or XML. The subset was chosen to be as simple as possible yet allow the expression of the kinds of data structures that need to be encoded in XML for the ERATO Kitano Systems Biology workbench." [cache]
