Systems Biology Ontology: Difference between revisions

Revision as of 00:51, 9 December 2024

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.

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.

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.

Structure

SBO is organized into several main categories, each representing a different aspect of systems biology:

Quantitative Parameters: Terms related to the numerical values used in models, such as rate constants and concentrations.
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.

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.

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.

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.

Also see

Template:Systems Biology

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-[[file:SBO_logo.png|thumb|SBO logo]] [[file:SBO_small.jpg|thumb|SBO small|left]] '''Systems Biology Ontology''' (SBO) is a structured controlled vocabulary for the field of [[systems biology]]. It provides a set of terms and relationships to describe the types of entities and processes used in systems biology models. SBO is designed to support the annotation of models in a consistent and unambiguous manner, facilitating data sharing and integration.
+[[File:SBO logo.png|thumb]] [[File:SBO small.jpg|thumb]] {{Infobox ontology
+| name = Systems Biology Ontology
+| acronym = SBO
+| description = A set of controlled, structured vocabularies for use in computational modeling of biological systems.
+| domain = Systems Biology
+| website = [https://www.ebi.ac.uk/sbo/main/ SBO Main Page]
+}}
+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.
 == Overview ==
-The Systems Biology Ontology is part of the broader effort to standardize the representation of biological knowledge. It is used to annotate models created using various [[modeling languages]] such as [[SBML]] (Systems Biology Markup Language) and [[CellML]]. SBO terms can describe a wide range of concepts, including:
+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.
-* [[Biological processes]]
+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.
-* [[Molecular interactions]]
-* [[Kinetic laws]]
-* [[Mathematical expressions]]
 == Structure ==
-SBO is organized hierarchically, with general terms at the top and more specific terms at the lower levels. This hierarchical structure allows for the precise annotation of model components. The main categories in SBO include:
+SBO is organized into several main categories, each representing a different aspect of systems biology:
-* '''Participants''': Entities involved in biological processes, such as [[genes]], [[proteins]], and [[metabolites]].
+* '''Quantitative Parameters''': Terms related to the numerical values used in models, such as rate constants and concentrations.
-* '''Interactions''': Types of interactions between participants, such as [[binding]], [[catalysis]], and [[transport]].
+* '''Modeling Frameworks''': Concepts describing the mathematical and computational approaches used to construct models, such as [[ordinary differential equations]] and [[stochastic models]].
-* '''Mathematical expressions''': Descriptions of the mathematical relationships governing the interactions, including [[rate laws]] and [[equations]].
+* '''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 systems biology models to ensure consistency and interoperability. It is particularly useful in the following areas:
+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.
-* [[Model annotation]]: Providing detailed descriptions of model components and their interactions.
+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.
-* [[Data integration]]: Facilitating the integration of data from different sources by using a common vocabulary.
-* [[Model validation]]: Ensuring that models are correctly annotated and conform to established standards.
-== Related Pages ==
+== Development and Maintenance ==
-* [[Systems biology]]
+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.
-* [[Systems Biology Markup Language]]
-* [[CellML]]
-* [[Biological process]]
-* [[Molecular interaction]]
-* [[Kinetic law]]
-* [[Mathematical expression]]
-== See Also ==
+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.
-* [[Ontology (information science)]]
-* [[Controlled vocabulary]]
-* [[Bioinformatics]]
-== References ==
+== Also see ==
-{{Reflist}}
+* [[Gene Ontology]]
+* [[BioModels Database]]
+* [[Systems Biology Markup Language]]
+* [[Open Biomedical Ontologies]]
+* [[European Bioinformatics Institute]]
-== External Links ==
+{{Systems Biology}}
-{{Commons category|Systems Biology Ontology}}
+{{Bioinformatics}}
-[[Category:Systems biology]]
+[[Category:Systems Biology]]
+[[Category:Ontologies]]
 [[Category:Bioinformatics]]
-[[Category:Ontologies]]
-[[Category:Controlled vocabularies]]
-{{medicine-stub}}