Systems Biology Ontology

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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.

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:

• Biological processes
• 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:

• Participants: Entities involved in biological processes, such as genes, proteins, and metabolites.
• Interactions: Types of interactions between participants, such as binding, catalysis, and transport.
• Mathematical expressions: Descriptions of the mathematical relationships governing the interactions, including rate laws and equations.

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:

• Model annotation: Providing detailed descriptions of model components and their interactions.
• 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

• Systems biology
• Systems Biology Markup Language
• CellML
• Biological process
• Molecular interaction
• Kinetic law
• Mathematical expression

See Also

• Ontology (information science)
• Controlled vocabulary
• Bioinformatics