SBO

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Motivation

The rise of Systems Biology, seeking to comprehend biological processes as a whole, highlighted the need to not only develop corresponding quantitative models, but also to create standards allowing their exchange and integration. This concern drove the community to design common data format such as SBML and CellML. SBML is now largely accepted and used in the field. However, as important as the definition of a common syntax is, it is also necessary to make clear the semantics of models. SBO is an attempt to provide the means of annotating models with terms that indicate the intended semantics of an important subset of models in common use in computational systems biology.

Structure

SBO is currently made up of five different vocabularies: quantitative parameters (catalytic constant, thermodynamic temperature ...), participant type (substrate, product, catalyst...), modelling frameworks (discrete, continuous...), mathematical expressions and events.

Resources

  To curate and maintain SBO, a dedicated resource has been developed and the public interface of the SBO browser can be accessed at http://www.ebi.ac.uk/sbo. A relational database management system (MySQL) at the back-end is accessed through a web interface based on Java Server Pages (JSP) and JavaBeans. Its content is encoded in UTF-8, therefore supporting a large set of characters in the definitions of terms. Distributed curation is made possible by using a custom-tailored locking system allowing concurrent access. This system allows a continuous update of the ontology with immediate availability and suppress merging problems.

Several exports formats (OBO flat file, SBO-XML and OWL) are generated daily or on request and can be downloaded from the web interface.

To allow programmatic access to the resource, Web Services have been implemented based on Apache Axis for the communication layer and Castor for the validation. The librairies, full documentation, samples and tutorial are available online.

The sourceforge project can be accessed at http://sourceforge.net/projects/sbo/.

SBO and SBML

SBML Level 2 Version 2 provides a mechanism to annotate model components with SBO terms, therefore increasing the semantics of the model beyond the sole topology of interaction and mathematical expression. Simulation tools can check the consistency of a rate law, convert reaction from one modelling framework to another (e.g., continuous to discrete), or distinguish between identical mathematical expressions based on different assumptions (e.g., Henri-Michaelis-Menten Vs. Briggs-Haldane). Other tools such as SBMLmerge can use the SBO annotation to integrate individual models into a larger one. The use of SBO is not restricted to the development of models. Resources providing quantitative experimental information such as SABIO Reaction Kinetics will be able to annotate the parameters (what do they mean exactly, how were they calculated) and determine relationships between them.

Organization of SBO development

SBO is built in collaboration by the Computational Neurobiology Group (Nicolas Le Novère, EMBL-EBI, United-Kingdom) and the SBMLTeam (Michael Hucka, Caltech, USA).

Funding for SBO

SBO has benefited from the funds of the European Molecular Biology Laboratory and the National Institute of General Medical Sciences.

External references

• www.biomodels.net
• [1] The Systems Biology Markup Language (SBML): A Medium for Representation and Exchange of Biochemical Network Models
• [2] CellML: its future, present and past.