Systems Biology Ontology

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:

• 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:

• 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

• Official SBO website
• Ontology Lookup Service for SBO

See Also

• Gene Ontology
• BioPAX
• CellML

Gallery

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