Systems Biology Ontology
The Systems Biology Ontology is a set of controlled, relational vocabularies of terms commonly used in systems biology, and in particular in computational modeling.
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 formats, 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 tries to give us a way to label models with words that describe how they should be used in a large group of models that are commonly used in computational systems biology. The development of SBO was first discussed at the 9th SBML Forum Meeting in Heidelberg on October 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:- systems description parameter
- participant role
- modelling framework
- mathematical expression
- occurring entity representation
- physical entity representation
- metadata representation
Resources
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 themodel beyond the sole topology of interaction and mathematical expression. Modelling tools such as interpret SBO terms to augment the mathematics in the SBML file. 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. To add missing SBO terms to models, software such as can be used. 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.