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CompartmentType_t Class Reference

Detailed Description

Implementation of SBML's Level 2's CompartmentType construct.

SBML Level 2 Versions 2–4 provide the compartment type as a grouping construct that can be used to establish a relationship between multiple Compartment objects. A CompartmentType object only has an identity, and this identity can only be used to indicate that particular Compartment objects in the model belong to this type. This may be useful for conveying a modeling intention, such as when a model contains many similar compartments, either by their biological function or the reactions they carry. Without a compartment type construct, it would be impossible within SBML itself to indicate that all of the compartments share an underlying conceptual relationship because each SBML compartment must be given a unique and separate identity. Compartment types have no mathematical meaning in SBML—they have no effect on a model's mathematical interpretation. Simulators and other numerical analysis software may ignore CompartmentType definitions and references to them in a model.

There is no mechanism in SBML Level 2 for representing hierarchies of compartment types. One CompartmentType instance cannot be the subtype of another CompartmentType instance; SBML provides no means of defining such relationships.

As with other major structures in SBML, CompartmentType has a mandatory attribute, "id", used to give the compartment type an identifier. The identifier must be a text string conforming to the identifer syntax permitted in SBML. CompartmentType also has an optional "name" attribute, of type string. The "id" and "name" must be used according to the guidelines described in the SBML specification (e.g., Section 3.3 in the Level 2 Version 4 specification).

CompartmentType was introduced in SBML Level 2 Version 2. It is not available in SBML Level 1 nor in Level 3.

See Also
Compartment
ListOfCompartmentTypes
SpeciesType
ListOfSpeciesTypes