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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.
 
{{Infobox ontology
| name = Systems Biology Ontology
| acronym = SBO
| description = A set of controlled, relational vocabularies of terms commonly used in systems biology, computational modeling, and quantitative biology.
| domain = Systems Biology
| website = [http://www.ebi.ac.uk/sbo/ 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 ==
== 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 is designed to support the annotation of models and simulations in systems biology. It includes terms for:


* [[Modeling frameworks]]
* [[Simulation algorithms]]
* [[Biological processes]]
* [[Biological processes]]
* [[Molecular interactions]]
* [[Quantitative parameters]]
* [[Kinetic laws]]
 
* [[Mathematical expressions]]
SBO is used by various systems biology tools and databases to ensure consistent annotation and to facilitate data exchange and integration.


== Structure ==
== 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:


* '''Participants''': Entities involved in biological processes, such as [[genes]], [[proteins]], and [[metabolites]].
* '''SBO:0000000''' - [[Root term]]
* '''Interactions''': Types of interactions between participants, such as [[binding]], [[catalysis]], and [[transport]].
* '''SBO:0000231''' - [[Quantitative systems description parameter]]
* '''Mathematical expressions''': Descriptions of the mathematical relationships governing the interactions, including [[rate laws]] and [[equations]].
* '''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 ==
== 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 the [[Systems Biology Markup Language]] (SBML) and other related standards. It helps in:


* [[Model annotation]]: Providing detailed descriptions of model components and their interactions.
* Ensuring consistent use of terminology across different models and databases.
* [[Data integration]]: Facilitating the integration of data from different sources by using a common vocabulary.
* Facilitating the sharing and reuse of models.
* [[Model validation]]: Ensuring that models are correctly annotated and conform to established standards.
* Enabling automated reasoning and analysis of models.


== Related Pages ==
== Development and Maintenance ==
* [[Systems biology]]
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.
* [[Systems Biology Markup Language]]
 
* [[CellML]]
== External Links ==
* [[Biological process]]
* [http://www.ebi.ac.uk/sbo/ Official SBO website]
* [[Molecular interaction]]
* [https://www.ebi.ac.uk/ols/ontologies/sbo Ontology Lookup Service for SBO]
* [[Kinetic law]]
* [[Mathematical expression]]


== See Also ==
== See Also ==
* [[Ontology (information science)]]
* [[Gene Ontology]]
* [[Controlled vocabulary]]
* [[BioPAX]]
* [[Bioinformatics]]
* [[CellML]]


== References ==
== Gallery ==
{{Reflist}}
<gallery>
 
File:SBO_logo.png|SBO logo
== External Links ==
</gallery>
{{Commons category|Systems Biology Ontology}}
[[Category:Systems Biology]]
 
[[Category:Ontologies]]
[[Category:Systems biology]]
[[Category:Bioinformatics]]
[[Category:Bioinformatics]]
[[Category:Ontologies]]
[[Category:Controlled vocabularies]]
{{medicine-stub}}

Latest revision as of 00:24, 25 February 2025

Template:Infobox 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[edit]

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[edit]

SBO is organized into several main categories:

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[edit]

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[edit]

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[edit]

See Also[edit]

Gallery[edit]

  • SBO logo
    SBO logo
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