SBO
Encyclopedia
The Systems Biology Ontology (SBO) 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 BioModels.net effort.
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.
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/.
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 to .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 semanticSBML 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.
, United-Kingdom) and the SBML
Team (Michael Hucka, Caltech, USA).
and the National Institute of General Medical Sciences
.
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 theirexchange and integration. This concern drove the community to design common data format such as SBML
SBML
The Systems Biology Markup Language is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers...
and CellML
CellML
CellML is an XML based markup language for describing mathematical models. Although it could theoretically describe any mathematical model, it was originally created with the Physiome Project in mind, and hence used primarily to describe models relevant to the field of biology...
. SBML
SBML
The Systems Biology Markup Language is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers...
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
SBML
The Systems Biology Markup Language is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers...
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:- systems description parameter (catalytic constant, thermodynamic temperature, …)
- participant role (substrate, product, catalyst, …)
- modelling framework (discrete, continuous…)
- mathematical expression (mass action rate law, Hill-type rate law, …)
- occurring entity representation (biochemical process, molecular or genetic interaction, …)
- physical entity representation (transporter, physical compartment, observable, …)
- metadata representation (annotation)
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
MySQL
MySQL officially, but also commonly "My Sequel") is a relational database management system that runs as a server providing multi-user access to a number of databases. It is named after developer Michael Widenius' daughter, My...
) at the back-end is
accessed through a web interface based on Java Server Pages (JSP) and JavaBeans
JavaBeans
JavaBeans are reusable software components for Java. Practically, they are classes written in the Java programming language conforming to a particular convention. They are used to encapsulate many objects into a single object , so that they can be passed around as a single bean object instead of as...
. Its
content is encoded in UTF-8
UTF-8
UTF-8 is a multibyte character encoding for Unicode. Like UTF-16 and UTF-32, UTF-8 can represent every character in the Unicode character set. Unlike them, it is backward-compatible with ASCII and avoids the complications of endianness and byte order marks...
, 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
Since Level 2 Version 2 SBMLSBML
The Systems Biology Markup Language is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers...
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 to .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 semanticSBML 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-EBIEuropean Bioinformatics Institute
The European Bioinformatics Institute is a centre for research and services in bioinformatics, and is part of European Molecular Biology Laboratory...
, United-Kingdom) and the SBML
SBML
The Systems Biology Markup Language is a representation format, based on XML, for communicating and storing computational models of biological processes. It is a free and open standard with widespread software support and a community of users and developers...
Team (Michael Hucka, Caltech, USA).
Funding for SBO
SBO has benefited from the funds of the European Molecular Biology LaboratoryEuropean Molecular Biology Laboratory
The European Molecular Biology Laboratory is a molecular biology research institution supported by 20 European countries and Australia as associate member state. EMBL was created in 1974 and is an intergovernmental organisation funded by public research money from its member states...
and the National Institute of General Medical Sciences
National Institute of General Medical Sciences
The National Institute of General Medical Sciences is a part of the National Institutes of Health that primarily supports research that lays the foundation for advances in disease diagnosis, treatment and prevention...
.