SBML

Systems Biology Markup Language (SBML)
Filename extension .xml, .sbml
Internet media type application/sbml+xml
Initial release 2 March 2001 (2001-03-02)
Latest release
SBML Level 3 Version 1 Core, Release 1
(6 October 2010 (2010-10-06))
Type of format Markup language
Extended from XML
Open format? Yes
Website sbml.org

The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes.[1] It is a free and open standard with widespread software support and a community of users and developers. SBML can represent many different classes of biological phenomena, including metabolic networks, cell signaling pathways, regulatory networks, infectious diseases, and many others.[2][3][4] It has been proposed as a standard for representing computational models in systems biology today.[4]

History

Late in the year 1999 through early 2000, with funding from the Japan Science and Technology Corporation (JST), Hiroaki Kitano and John C. Doyle assembled a small team of researchers to work on developing better software infrastructure for computational modeling in systems biology. Hamid Bolouri was the leader of the development team, which consisted of Andrew Finney, Herbert Sauro, and Michael Hucka.[5] Bolouri identified the need for a framework to enable interoperability and sharing between the different simulation software systems for biology in existence during the late 1990s, and he organized an informal workshop in December 1999 at the California Institute of Technology to discuss the matter. In attendance at that workshop were the groups responsible for the development of DBSolve, E-Cell, Gepasi, Jarnac, StochSim and The Virtual Cell. Separately, earlier in 1999, some members of these groups also had discussed the creation of a portable file format for metabolic network models in the BioThermoKinetics (BTK) group.[6][7] The same groups who attended the first Caltech workshop met again on April 28–29, 2000, at the first of a newly created meeting series called Workshop on Software Platforms for Systems Biology.[8] It became clear during the second workshop that a common model representation format was needed to enable the exchange of models between software tools as part of any functioning interoperability framework, and the workshop attendees decided the format should be encoded in XML.

The Caltech ERATO team developed a proposal for this XML-based format and circulated the draft definition to the attendees of the 2nd Workshop on Software Platforms for Systems Biology in August, 2000. This draft underwent extensive discussion over mailing lists and during the 2nd Workshop on Software Platforms for Systems Biology,[9] held in Tokyo, Japan, in November 2000 as a satellite workshop of the ICSB 2000 conference. After further revisions, discussions and software implementations, the Caltech team issued a specification for SBML Level 1, Version 1 in March, 2001.

SBML Level 2 was conceived at the 5th Workshop on Software Platforms for Systems Biology, held in July 2002, at the University of Hertfordshire, UK.[10] By this time, far more people were involved than the original group of SBML collaborators and the continued evolution of SBML became a larger community effort, with many new tools having been enhanced to support SBML. The workshop participants in 2002 collectively decided to revise the form of SBML in Level 2. The first draft of the Level 2 Version 1 specification was released in August 2002, and the final set of features was finalized in May 2003 at the 7th Workshop on Software Platforms for Systems Biology in Ft. Lauderdale, Florida.

The next iteration of SBML took two years in part because software developers requested time to absorb and understand the larger and more complex SBML Level 2. The inevitable discovery of limitations and errors led to the development of SBML Level 2 Version 2, issued in September 2006. By this time, the team of SBML Editors (who reconcile proposals for changes and write a coherent final specification document) had changed and now consisted of Andrew Finney, Michael Hucka and Nicolas Le Novère.

SBML Level 2 Version 3 was published in 2007 after countless contributions by and discussions with the SBML community. 2007 also saw the election of two more SBML Editors as part of the introduction of the modern SBML Editor organization in the context of the SBML development process.

SBML Level 2 Version 4 was published in 2008 after certain changes in Level 2 were requested by popular demand. (For example, an electronic vote by the SBML community in late 2007 indicated a majority preferred not to require strict unit consistency before an SBML model is considered valid.) Version 4 was finalized after the SBML Forum meeting held in Gothenburg, Sweden, as a satellite workshop of ICSB 2008 in the fall of 2008.[11]

SBML Level 3 Version 1 Core was published in final form in 2010, after prolonged discussion and revision by the SBML Editors and the SBML community. It contains numerous significant changes in syntax and constructs from Level 2 Version 4, but also represents a new modular base for continued expansion of SBML's features and capabilities going into the future.

SBML Level 2 Version 5 was published in 2015. This revision included a number of textual (but not structural) changes in response to user feedback, thereby addressing the list of errata collected over many years for the SBML Level 2 Version 4 specification. In addition, Version 5 introduced a facility to use nested annotations within SBML's annotation format (an annotation format that is based on a subset of RDF).

The language

SBML is sometimes incorrectly assumed to be limited in scope only to biochemical network models because the original publications and early software focused on this domain. In reality, although the central features of SBML are indeed oriented towards representing chemical reaction-like processes that act on entities, this same formalism serves analogously for many other types of processes; moreover, SBML has language features supporting the direct expression of mathematical formulas and discontinuous events separate from reaction processes, allowing SBML to represent much more than solely biochemical reactions. Evidence for SBML's ability to be used for more than merely descriptions of biochemistry can be seen in the variety of models available from BioModels Database.

Purposes

SBML has three main purposes:

SBML is not an attempt to define a universal language for quantitative models. SBML's purpose is to serve as a lingua franca—an exchange format used by different present-day software tools to communicate the essential aspects of a computational model.[12]

Main capabilities

SBML can encode models consisting of entities (called species in SBML) acted upon by processes (called reactions). An important principle is that models are decomposed into explicitly-labeled constituent elements, the set of which resembles a verbose rendition of chemical reaction equations (if the model uses reactions) together with optional explicit equations (again, if the model uses these); the SBML representation deliberately does not cast the model directly into a set of differential equations or other specific interpretation of the model. This explicit, modeling-framework-agnostic decomposition makes it easier for a software tool to interpret the model and translate the SBML form into whatever internal form the tool actually uses.

A software package can read an SBML model description and translate it into its own internal format for model analysis. For example, a package might provide the ability to simulate the model by constructing differential equations and then perform numerical time integration on the equations to explore the model's dynamic behavior. Or, alternatively, a package might construct a discrete stochastic representation of the model and use a Monte Carlo simulation method such as the Gillespie algorithm.

SBML allows models of arbitrary complexity to be represented. Each type of component in a model is described using a specific type of data structure that organizes the relevant information. The data structures determine how the resulting model is encoded in XML.

In addition to the elements above, another important feature of SBML is that every entity can have machine-readable annotations attached to it. These annotations can be used to express relationships between the entities in a given model and entities in external resources such as databases. A good example of the value of this is in BioModels Database, where every model is annotated and linked to relevant data resources such as publications, databases of compounds and pathways, controlled vocabularies, and more. With annotations, a model becomes more than simply a rendition of a mathematical construct—it becomes a semantically-enriched framework for communicating knowledge.[13][14]

Levels and versions

SBML is defined in Levels: upward-compatible specifications that add features and expressive power. Software tools that do not need or cannot support the complexity of higher Levels can go on using lower Levels; tools that can read higher Levels are assured of also being able to interpret models defined in the lower Levels. Thus new Levels do not supersede previous ones. However, each Level can have multiple Versions within it, and new Versions of a Level do supersede old Versions of that same Level.

There are currently three Levels of SBML defined. The current Versions within those Levels are the following:

Open-source software infrastructure such as libSBML and JSBML allows developers to support all Levels of SBML their software with a minimum amount of effort.

The SBML Team maintains a public issue tracker where readers may report errors or other issues in the SBML specification documents. Reported issues are eventually put on the list of official errata associated with each specification release. The lists of errata are documented on the Specifications page of SBML.org.

Level 3 packages

Development of SBML Level 3 has been proceeding in a modular fashion. The Core specification is a complete format that can be used alone. Additional Level 3 packages can be layered on to this core to provide additional, optional features.

Hierarchical Model Composition

The Hierarchical Model Composition package, known as "comp", was released in November 2012. This package provides the ability to include models as submodels inside another model. The goal is to support the ability of modelers and software tools to do such things as (1) decompose larger models into smaller ones, as a way to manage complexity; (2) incorporate multiple instances of a given model within one or more enclosing models, to avoid literal duplication of repeated elements; and (3) create libraries of reusable, tested models, much as is done in software development and other engineering fields. The specification was the culmination of years of discussion by a wide number of people.

Flux Balance Constraints

The Flux Balance Constraints package (nicknamed "fbc") was first released in February, 2013. Import revisions were introduced as part of Version 2,[15] released in September, 2015. The "fbc" package provides support for constraint based modeling,[16] frequently used to analyze and study biological networks on both a small and large scale.[17] This SBML package makes use of standard components from the SBML Level 3 core specification, including species and reactions, and extends them with additional attributes and structures to allow modelers to define such things as flux bounds and optimization functions.

Qualitative Models

The Qualitative Models or "qual" package for SBML Level 3 was released in May, 2013. This package supports the representation of models where an in-depth knowledge of the biochemical reactions and their kinetics is missing and a qualitative approach must be used. Examples of phenomena that have been modeled in this way include gene regulatory networks [18] and signalling pathways,[19] basing the model structure on the definition of regulatory or influence graphs. The definition and use of some components of this class of models differ from the way that species and reactions are defined and used in core SBML models. For example, qualitative models typically associate discrete levels of activities with entity pools; consequently, the processes involving them cannot be described as reactions per se, but rather as transitions between states. These systems can be viewed as reactive systems whose dynamics are represented by means of state transition graphs (or other Kripke structures [20]) in which the nodes are the reachable states and the edges are the state transitions.

Layout

The SBML layout package originated as a set of annotation conventions usable in SBML Level 2. It was introduced at the SBML Forum in St. Louis in 2004.[21] Ralph Gauges wrote the specification [22] and provided an implementation that was widely used. This original definition was reformulated as an SBML Level 3 package, and a specification was formally released in August, 2013.

The SBML Level 3 Layout package provides a specification for how to represent a reaction network in a graphical form. It is thus better tailored to the task than the use of an arbitrary drawing or graph. The SBML Level 3 package only deals with the information necessary to define the position and other aspects of a graph's layout; the additional details necessary to complete the graph—namely, how the visual aspects are meant to be rendered— are the purvey of the separate SBML Level 3 package called Rendering (nicknamed "render"). As of November 2015, a draft specification for the "render" package is available, but it has not yet been officially finalized.[23]

Packages under development

Development of SBML Level 3 packages is being undertaken such that specifications are reviewed and implementations attempted during the development process. Once a specification is a stable and there are two implementations that support it, the package is considered accepted. The packages detailed above have all reached the accepted stage. The table below gives a brief summary of packages that are currently in the development phase.

Package name Label Description
Arrays arrays Support for expressing arrays of components
Distributions distrib Support for encoding models that sample values from statistical distributions or specify statistics associated with numerical values
Dynamics dyn Support for creating and destroying entities during a simulation
Groups groups A means for grouping elements
Multistate and Multicomponent species multi Object structures for representing entity pools with multiple states and composed of multiple components, and reaction rules involving them
Rendering render Support for defining the graphical symbols and glyphs used in a diagram of the model; adjunct to the layout package
Required Elements req Support for fine-grained indication of SBML elements that have been changed by the presence of another package
Spatial Processes spatial Support for describing processes that involve a spatial component, and describing the geometries involved

Structure

A model definition in SBML Levels 2 and 3 consists of lists of one or more of the following components:

Community

As of September, 2015, more than 280 software systems advertise support for SBML. A current list is available in the form of the SBML Software Guide, hosted at SBML.org.

SBML has been and continues to be developed by the community of people making software platforms for systems biology, through active email discussion lists and biannual workshops. The meetings are often held in conjunction with other biology conferences, especially the International Conference on Systems Biology (ICSB). The community effort is coordinated by an elected editorial board made up of five members. Each editor is elected for a 3-year non-renewable term.

Tools such as an online model validator as well as open-source libraries for incorporating SBML into software programmed in the C, C++, Java, Python, Mathematica, MATLAB and other languages are developed partly by the SBML Team and partly by the broader SBML community.[24]

SBML is an official IETF MIME type, specified by RFC 3823.[25]

See also

References

  1. ↑ Encyclopedia of Systems Biology Dubitzky, W., Wolkenhauer, O., Yokota, H., Cho, K.-H. (Eds.) SBML, pp2057-2062 Springer 2013 ISBN 978-1-4419-9863-7
  2. ↑ Hucka, M.; Finney, A.; Sauro, H. M.; Bolouri, H.; Doyle, J. C.; Kitano, H.; Arkin, A. P.; Bornstein, A. P.; Bray, B. J.; Cornish-Bowden, D.; Cuellar, A.; Dronov, A. A.; Gilles, S.; Ginkel, E. D.; Gor, M.; Goryanin, V.; Hedley, I. I.; Hodgman, W. J.; Hofmeyr, T. C.; Hunter, J. -H.; Juty, P. J.; Kasberger, N. S.; Kremling, J. L.; Kummer, A.; Le Novère, U.; Loew, N.; Lucio, L. M.; Mendes, P.; Minch, P.; Mjolsness, E. (2003). "The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models". Bioinformatics 19 (4): 524–531. doi:10.1093/bioinformatics/btg015. PMID 12611808.
  3. ↑ Finney, A.; Hucka, M. (2003). "Systems biology markup language: Level 2 and beyond". Biochemical Society Transactions 31 (6): 1472. doi:10.1042/BST0311472.
  4. 1 2 Hucka, M.; Finney, A.; Bornstein, B. J.; Keating, S. M.; Shapiro, B. E.; Matthews, J.; Kovitz, B. L.; Schilstra, M. J.; Funahashi, A.; Doyle, S. M.; Kitano, M. J. (2004). "Evolving a lingua franca and associated software infrastructure for computational systems biology: The Systems Biology Markup Language (SBML) project". Systems Biology 1 (1): 41–53. doi:10.1049/sb:20045008. PMID 17052114.
  5. ↑ Hucka, Michael. "History of SBML". Retrieved 3 January 2010.
  6. ↑ bionet.metabolic-reg. "ANNOUNCEMENT: Portable Metabolic Binary Standard". Retrieved 13 December 2010.
  7. ↑ Kell, D. B.; Mendes, P. (2008). "The markup is the model: Reasoning about systems biology models in the Semantic Web era". Journal of Theoretical Biology 252 (3): 538–543. doi:10.1016/j.jtbi.2007.10.023. PMID 18054049.
  8. ↑ SBML Team. "The 1st Workshop on Software Platforms for Systems Biology". Retrieved 3 December 2010.
  9. ↑ SBML Team. "The 2nd Workshop on Software Platforms for Systems Biology". Retrieved 13 December 2010.
  10. ↑ SBML Team. "The 5th Workshop on Software Platforms for Systems Biology". Retrieved 3 January 2010.
  11. ↑ SBML Team. "The 13th SBML Forum". Retrieved 3 January 2010.
  12. ↑ Finney, A., Hucka, M., Bornstein, B.J., Keating, S.M., Shapiro, B.E., Matthews, J., Kovitz, B.L., Schilstra, M.J., Funahashi, A., Doyle, J.C., Kitano, H. (2006). "Software Infrastructure for Effective Communication and Reuse of Computational Models". Systems Modeling in Cell Biology: From Concepts to Nuts and Bolts. MIT Press. pp. 369–378.
  13. ↑ Krause, Falko; Uhlendorf, Jannis; Lubitz, Timo; Schulz, Marvin; Klipp, Edda; Liebermeister, Wolfram (2009). "Annotation and merging of SBML models with semanticSBML". Bioinformatics 26 (3): 421–2. doi:10.1093/bioinformatics/btp642. PMID 19933161.
  14. ↑ Alm, Rebekka; Waltemath, Dagmar; Wolfien, Markus; Wolkenhauer, Olaf; Henkel, Ron (2015). "Annotation-based feature extraction from sets of SBML models". Journal of Biomedical Semantics 6. doi:10.1186/s13326-015-0014-4.
  15. ↑ Brett G. Olivier and Frank T. Bergmann. "SBML Level 3 Package: Flux Balance Constraints (‘fbc’)". Retrieved 24 November 2015.
  16. ↑ Orth, Jeffrey D; Thiele, Ines; Palsson, Bernhard O (2010). "What is flux balance analysis?". Nature Biotechnology 28 (3): 245–8. doi:10.1038/nbt.1614. PMC 3108565. PMID 20212490.
  17. ↑ Oberhardt, Matthew A; Palsson, Bernhard O; Papin, Jason A (2009). "Applications of genome-scale metabolic reconstructions". Molecular Systems Biology 5. doi:10.1038/msb.2009.77.
  18. ↑ Batt, Gregory; Ropers, Delphine; de Jong, Hidde; Geiselmann, Johannes; Mateescu, Radu; Page, Michel; Schneider, Dominique (2005). "Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli". Bioinformatics 21: i19–28. doi:10.1093/bioinformatics/bti1048. PMID 15961457.
  19. ↑ Helikar, Tomas; Konvalina, John; Heidel, Jack; Rogers, Jim A (2008). "Emergent decision-making in biological signal transduction networks". Proceedings of the National Academy of Sciences 105 (6): 1913. doi:10.1073/pnas.0705088105.
  20. ↑ Clarke, E.M., Grumberg, O., Peled, DA (1999). Modal Checking. MIT Press.
  21. ↑ SBML Team. "The 8th SBML Forum". Retrieved 3 January 2010.
  22. ↑ Gauges, Ralph; Rost, Ursula; Sahle, Sven; Wegner, Katja (2006). "A model diagram layout extension for SBML". Bioinformatics 22 (15): 1879–85. doi:10.1093/bioinformatics/btl195. PMID 16709586.
  23. ↑ Ralph Gauges, Sven Sahle, Katjia Wengler, Frank T. Bergmann, and Sarah M. Keating. "SBML Level 3 Package: Rendering (‘render’)". Retrieved 24 November 2015.
  24. ↑ Rodriguez, Nicolas; Pettit, Jean-Baptiste; Dalle Pezze, Piero; Li, Lu; Henry, Arnaud (2016). "The systems biology format converter". BMC Bioinformatics 17 (1): 1–7. doi:10.1186/s12859-016-1000-2.
  25. ↑ Kovitz, Benjamin (June 2004). "MIME Media Type for the Systems Biology Markup Language (SBML).". IETF Request for Comments 3823. Retrieved 3 January 2010.

External links

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