Systems Biology Ontology project
SBO is the Systems Biology Ontology project, another cornerstone of the BioModels.net effort. The goal of SBO is to develop Controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems biology, especially in the context of 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 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 event.

# 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 (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 /.

# 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.

# How can I contribute
You are very welcome to propose terms.  In order to do so, please use the term tracker. There is also a mailing-list for more general discussions about SBO.

# Organization of SBO development
SBO is built in collaboration by the Computational Neurobiology Group (Nicolas Le Novere, 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
-  The Systems Biology Markup Language (SBML): A Medium for Representation and Exchange of Biochemical Network Models
-  CellML: its future, present and past.