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 th
BioModels.neteffort.
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
The Systems Biology Markup Language (SBML) 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 use ...
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
Pedro is a masculine given name. Pedro is the Spanish, Portuguese, and Galician name for ''Peter''. Its French equivalent is Pierre while its English and Germanic form is Peter.
The counterpart patronymic surname of the name Pedro, meaning ...
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 a
http://www.ebi.ac.uk/sbo
A relational database management system (
MySQL
MySQL () is an open-source relational database management system (RDBMS). Its name is a combination of "My", the name of co-founder Michael Widenius's daughter My, and "SQL", the acronym for Structured Query Language. A relational database ...
) at the back-end is
accessed through a web interface based on
Java Server Pages
Jakarta Server Pages (JSP; formerly JavaServer Pages) is a collection of technologies that helps software developers create dynamically generated web pages based on HTML, XML, SOAP, or other document types. Released in 1999 by Sun Microsystems, J ...
(JSP) and
JavaBeans. Its
content is encoded in
UTF-8
UTF-8 is a variable-length character encoding used for electronic communication. Defined by the Unicode Standard, the name is derived from ''Unicode'' (or ''Universal Coded Character Set'') ''Transformation Format 8-bit''.
UTF-8 is capable of ...
, 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
OBOflat file
SBO-XMLan
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 o
Apache Axisfor the communication layer an
Castorfor the validation. The libraries, full documentation, samples and tutorial are availabl
The SourceForge project can be accessed a
http://sourceforge.net/projects/sbo/
SBO and SBML
Sinc
Level 2 Version 2SBML
The Systems Biology Markup Language (SBML) 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 use ...
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 (e.g., continuous to discrete), or distinguish between identical mathematical expressions based on different assumptions (e.g., Michaelis–Menten vs. Briggs–Haldane). Other tools such a
semanticSBMLref>Krause F, Uhlendorf J., Lubitz T., Schulz M., Klipp E., Liebermeister W. (2010), Annotation and merging of SBML models with semanticSBML, Bioinformatics 26 (3), 421-422 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 a
SABIO Reaction Kineticswill be able to annotate the parameters (what do they mean exactly, how were they calculated) and determine relationships between them.
SBO and SBGN
All the graphical symbols used in the
SBGN
The Systems Biology Graphical Notation (SBGN) is a standard graphical representation intended to foster the efficient storage, exchange and reuse of information about signaling pathways, metabolic networks, and gene regulatory networks amongst com ...
languages are associated with an SBO term. This permits, for instance, to help generate
SBGN
The Systems Biology Graphical Notation (SBGN) is a standard graphical representation intended to foster the efficient storage, exchange and reuse of information about signaling pathways, metabolic networks, and gene regulatory networks amongst com ...
maps from
SBML
The Systems Biology Markup Language (SBML) 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 use ...
models.
SBO and BioPAX
The Systems Biology Pathway Exchange (SBPAX) allows SBO terms to be added to
Biological Pathway Exchange (BioPAX). 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 th
Computational Neurobiology Group(Nicolas Le Novère,
EMBL-
EBI, United-Kingdom) and the
SBML
The Systems Biology Markup Language (SBML) 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 use ...
Team (Michael Hucka,
Caltech
The California Institute of Technology (branded as Caltech or CIT)The university itself only spells its short form as "Caltech"; the institution considers other spellings such a"Cal Tech" and "CalTech" incorrect. The institute is also occasional ...
, USA).
Funding for SBO
SBO has benefited from the funds of the
European Molecular Biology Laboratory
The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 27 member states, two prospect states, and one associate member state. EMBL was created in 1974 and ...
and the
National Institute of General Medical Sciences
The National Institute of General Medical Sciences (NIGMS) supports basic research that increases understanding of biological processes and lays the foundation for advances in disease diagnosis, treatment, and prevention. NIGMS-funded scientists ...
.
References
External links
www.biomodels.net*
*
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