Systems Biology Ontology: Difference between revisions

Revision as of 21:47, 29 December 2024

The Systems Biology Ontology (SBO) is a structured controlled vocabulary for the field of systems biology. It provides a set of terms and relationships that are used to describe models, simulations, and data in a standardized way. This ontology is crucial for ensuring that different systems biology resources can interoperate and that data can be shared and understood across different platforms and studies.

Overview

The Systems Biology Ontology is designed to support the annotation of models and simulations in systems biology. It includes terms for:

SBO is used by various systems biology tools and databases to ensure consistent annotation and to facilitate data exchange and integration.

Structure

SBO is organized into several main categories:

SBO:0000000 - Root term
SBO:0000231 - Quantitative systems description parameter
SBO:0000293 - Modeling framework
SBO:0000545 - Simulation algorithm

Each term in SBO is assigned a unique identifier and is defined with a precise meaning. The ontology is hierarchical, allowing for terms to have parent-child relationships, which helps in organizing the terms in a meaningful way.

Applications

SBO is widely used in the annotation of models in the Systems Biology Markup Language (SBML) and other related standards. It helps in:

Ensuring consistent use of terminology across different models and databases.
Facilitating the sharing and reuse of models.
Enabling automated reasoning and analysis of models.

Development and Maintenance

The Systems Biology Ontology is developed and maintained by the European Bioinformatics Institute (EBI). It is an open resource, and contributions from the community are encouraged to ensure that it remains comprehensive and up-to-date.

External Links

References

,

 The Systems Biology Ontology, 
 Nature Biotechnology, 
 2005,
 Vol. 23(Issue: 12),
 pp. 1509–1510,
 DOI: 10.1038/nbt1156,

@@ Line 1: / Line 1: @@
-[[File:SBO logo.png|thumb]] [[File:SBO small.jpg|thumb]] {{Infobox ontology
+{{Infobox ontology
 | name = Systems Biology Ontology
 | acronym = SBO
-| description = A set of controlled, structured vocabularies for use in computational modeling of biological systems.
+| description = A set of controlled, relational vocabularies of terms commonly used in systems biology, computational modeling, and quantitative biology.
 | domain = Systems Biology
-| website = [https://www.ebi.ac.uk/sbo/main/ SBO Main Page]
+| website = [http://www.ebi.ac.uk/sbo/ Systems Biology Ontology]
 }}
-The '''Systems Biology Ontology''' (SBO) is a structured controlled vocabulary designed to provide a standardized framework for the annotation of computational models in the field of [[systems biology]]. It facilitates the consistent description of biological concepts and processes, enabling researchers to share and integrate data more effectively.
+The '''Systems Biology Ontology''' ('''SBO''') is a structured controlled vocabulary for the field of [[systems biology]]. It provides a set of terms and relationships that are used to describe models, simulations, and data in a standardized way. This ontology is crucial for ensuring that different systems biology resources can interoperate and that data can be shared and understood across different platforms and studies.
 == Overview ==
-The Systems Biology Ontology was developed to address the need for a common language in the rapidly growing field of systems biology. It provides a set of terms and relationships that can be used to annotate models, ensuring that they are interpretable and reusable by different researchers and software tools.
+The Systems Biology Ontology is designed to support the annotation of models and simulations in systems biology. It includes terms for:
-SBO is part of the [[Open Biomedical Ontologies]] (OBO) Foundry, which is a collaborative initiative to develop interoperable ontologies for the biological and biomedical sciences. The ontology is maintained by the [[European Bioinformatics Institute]] (EBI) and is freely available for use by the scientific community.
+* [[Modeling frameworks]]
+* [[Simulation algorithms]]
+* [[Biological processes]]
+* [[Quantitative parameters]]
+SBO is used by various systems biology tools and databases to ensure consistent annotation and to facilitate data exchange and integration.
 == Structure ==
-SBO is organized into several main categories, each representing a different aspect of systems biology:
+SBO is organized into several main categories:
+* '''SBO:0000000''' - [[Root term]]
+* '''SBO:0000231''' - [[Quantitative systems description parameter]]
+* '''SBO:0000293''' - [[Modeling framework]]
+* '''SBO:0000545''' - [[Simulation algorithm]]
-* '''Quantitative Parameters''': Terms related to the numerical values used in models, such as rate constants and concentrations.
+Each term in SBO is assigned a unique identifier and is defined with a precise meaning. The ontology is hierarchical, allowing for terms to have parent-child relationships, which helps in organizing the terms in a meaningful way.
-* '''Modeling Frameworks''': Concepts describing the mathematical and computational approaches used to construct models, such as [[ordinary differential equations]] and [[stochastic models]].
-* '''Biological Entities''': Terms for the components of biological systems, including [[genes]], [[proteins]], and [[metabolites]].
-* '''Interactions''': Descriptions of the relationships and interactions between biological entities, such as [[binding]], [[catalysis]], and [[inhibition]].
-* '''Phenomena''': Higher-level biological processes and phenomena, such as [[signal transduction]] and [[metabolic pathways]].
 == Applications ==
-SBO is widely used in the annotation of models in databases such as the [[BioModels Database]], which is a repository of computational models of biological processes. By using SBO terms, models can be more easily compared, shared, and integrated with other data sources.
+SBO is widely used in the annotation of models in the [[Systems Biology Markup Language]] (SBML) and other related standards. It helps in:
-The ontology also supports the development of software tools for systems biology, providing a common framework for the interpretation and analysis of model data. This enhances the ability of researchers to simulate and predict the behavior of complex biological systems.
+* Ensuring consistent use of terminology across different models and databases.
+* Facilitating the sharing and reuse of models.
+* Enabling automated reasoning and analysis of models.
 == Development and Maintenance ==
-The development of SBO is an ongoing process, with new terms and relationships being added as the field of systems biology evolves. The ontology is curated by a team of experts who ensure that it remains up-to-date and relevant to the needs of the scientific community.
+The Systems Biology Ontology is developed and maintained by the [[European Bioinformatics Institute]] (EBI). It is an open resource, and contributions from the community are encouraged to ensure that it remains comprehensive and up-to-date.
-Researchers are encouraged to contribute to the development of SBO by suggesting new terms or modifications to existing ones. This collaborative approach helps to ensure that the ontology reflects the latest advances in systems biology research.
+== External Links ==
+* [http://www.ebi.ac.uk/sbo/ Official SBO website]
+* [https://www.ebi.ac.uk/ols/ontologies/sbo Ontology Lookup Service for SBO]
-== Also see ==
+== See Also ==
 * [[Gene Ontology]]
-* [[BioModels Database]]
+* [[BioPAX]]
-* [[Systems Biology Markup Language]]
+* [[CellML]]
-* [[Open Biomedical Ontologies]]
-* [[European Bioinformatics Institute]]
-{{Systems Biology}}
+== References ==
-{{Bioinformatics}}
+* {{cite journal |last1=Le Novere |first1=Nicolas |title=The Systems Biology Ontology |journal=Nature Biotechnology |volume=23 |issue=12 |year=2005 |pages=1509–1510 |doi=10.1038/nbt1156}}
 [[Category:Systems Biology]]
 [[Category:Ontologies]]
 [[Category:Bioinformatics]]