SBO

, especially in the context of computational modeling.

Motivation

The rise of Systems Biology, seeking to comprehend biological processesas a whole, highlighted the need to not only develop correspondingquantitative models, but also to create standards allowing theirexchange and integration. This concern drove the community to designcommon data format such as SBML and CellML. SBML is nowlargely 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 themeans of annotating models with terms that indicate the intendedsemantics of an important subset of models in common use incomputational systems biology.

tructure

SBO is currently made up of five different vocabularies:quantitative parameters (catalytic constant, thermodynamic temperature...), participant type (substrate, product, catalyst...), modellingframeworks (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 http://www.ebi.ac.uk/sbo] . A relational database management system (MySQL) at the back-end isaccessed through a web interface based on Java Server Pages (JSP) and JavaBeans. Itscontent is encoded in UTF-8, therefore supporting a large set ofcharacters in the definitions of terms. Distributed curation is made possibleby using a custom-tailored locking system allowing concurrent access.This system allows a continuous update of the ontology with immediateavailability and suppress merging problems.

Several exports formats ( [http://www.godatabase.org/dev/doc/obo_format_spec.html OBO] flat file, [http://www.ebi.ac.uk/sbo/docs/sboxml_schema.xsd SBO-XML] and [http://www.w3.org/TR/owl-features/ 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 [http://ws.apache.org/axis/ Apache Axis] for the communication layer and [http://www.castor.org/ Castor] for the validation. The librairies, full documentation, samples and tutorial are available [http://www.ebi.ac.uk/sbo/SBOWSLib/ws.html online] .

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

SBO and SBML

[http://sourceforge.net/project/showfiles.php?group_id=71971&package_id=76633 SBML Level 2 Version 2] provides a mechanism to annotate modelcomponents with SBO terms, therefore increasing the semantics of themodel beyond the sole topology of interaction and mathematicalexpression. 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 mathematicalexpressions based on different assumptions (e.g.,Henri-Michaelis-Menten Vs. Briggs-Haldane). Other tools such as [http://sysbio.molgen.mpg.de/sbmlmerge/ SBMLmerge] can use the SBO annotation to integrate individual modelsinto a larger one. The use of SBO is not restricted to thedevelopment of models. Resources providing quantitative experimentalinformation such as [http://sabio.villa-bosch.de/SABIORK/ SABIO Reaction Kinetics] will be able to annotatethe 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 [http://www.ebi.ac.uk/compneur 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

* [http://biomodels.net www.biomodels.net]
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=12611808] The Systems Biology Markup Language (SBML): A Medium for Representation and Exchange of Biochemical Network Models
* [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids=15142756&dopt=Abstract] CellML: its future, present and past.