The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in Systems Biology, and in particular in computational modeling. SBO is part of the effort.
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. The development of SBO was first discussed at the 9th SBML Forum Meeting in Heidelberg Oct. 14–15, 2004. During the forum, Pedro Mendes mentioned that modellers possessed a lot of knowledge that was necessary to understand the model, and more importantly to simulate it, but this knowledge was not encoded in SBML. Nicolas Le Novère proposed to create a controlled vocabulary to store the content of Pedro Mendes' mind before he wandered out of the community. The development of the ontology was announced more officially in a message from Le Novère to Michael Hucka and Andrew Finney on October 19.
Structure
SBO is currently made up of seven different vocabularies:
To curate and maintain SBO, a dedicated resource has been developed and the public interface of the SBO browser can be accessed at . A relational database management system at the back-end is accessed through a web interface based on Java Server Pages 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 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 for the communication layer and for the validation. The libraries, full documentation, samples and tutorial are available . The sourceforge project can be accessed at .
SBO and SBML
Since SBML 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. Modelling tools such as SBMLsqueezer use SBO terms too. Simulation tools can check the consistency of a rate law, convert reaction from one modelling framework to another, or distinguish between identical mathematical expressions based on different assumptions. Other tools such as 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 will be able to annotate the parameters and determine relationships between them.
All the graphical symbols used in the SBGN languages are associated with an SBO term. This permits, for instance, to help generate SBGN maps from SBML models.
SBO and BioPAX
The Systems Biology Pathway Exchange allows SBO terms to be added to Biological Pathway Exchange. This links BioPAX to information useful for modelling, especially by adding quantitative descriptions described by SBO.
Organization of SBO development
SBO is built in collaboration by the and the SBMLTeam.
