Systems Biology Ontology

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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

• Gene Ontology
• BioModels Database
• Systems Biology Markup Language
• Open Biomedical Ontologies
• European Bioinformatics Institute