We are currently updating this wiki page. Only the UML diagrams are up to date, but NEITHER the description text NOR the examples.
SpeciesType, which was part of SBML Level 2 specification, will not be part of SBML Level 3 any more, instead it will be contained within the multi package. The
SpeciesType element carries not only the basic attributes which it had before but is also extended for the needs of the extension.
Apart from an ID, a name, and several annotations, it is furthermore possible to define
BindingSites. The following UML diagram shows how the structure of the
SpeciesType looks like.
SpeciesType can carry any number of
StateFeatures which are characteristic attributes specific for this type of species. After discussions between all to this extension contributing parties, it has been decided, that a
StateFeature is NOT the same as a
BindingSite. The reason for that decision is that a
BindingSite can carry attributes specific to itself which is not necessary for a
StateFeature also requires the definition of
PossibleValues which will be used within an
Selectors to define the state of an entity which i.e. could then be used as a condition for a
StateFeature is not obligatory a boolean property, but can take any number of possible values.
To show the usage of
StateFeatures the above given example of the receptor pore shall be used. In this example, the
StateFeature is the pore with the
PossibleValues being open, closed and desensitized. The SBML code for defining this
SpeciesType would look like the following
<speciesType xmlns="http://www.sbml.org/sbml/level3/version1/multi/version1" id="speciesType_1" name="example species Type 1"> <listOfStateFeatures> <stateFeature id="pore"> <listOfPossibleValues> <possibleValue id="open" /> <possibleValue id="closed" /> <possibleValue id="desensitized" /> </listOfPossibleValues> </stateFeature> </listOfStateFeatures> </speciesType>
In addition to
SpeciesType can carry different
BindingSites. A specific
BindingSite can be present several times on a
SpeciesType, and this number can vary in a defined way. This does not mean one can create or destroy
BindingSites during a simulation. The variability is needed for different instances of the
SpeciesType (as selected by a
Selector) having different numbers of a given
BindingSite. The attributes
maxOccur define the minimal and maximal number of this specific
BindingSite which can exist over all instances. If the
BindingSite should only exist once, it is required to set both these attributes to "1".
More information about the different states of binding sites and how to use them can be found here .
<speciesType xmlns="http://www.sbml.org/sbml/level3/version1/multi/version1" id="speciesType_2" name="example SpeciesType with BindingSite"> <listOfBindingSites> <bindingSite id="bindingSite_1" name="example binding site 1" minOccur="1" maxOccur="1"/> <listOfBindingSites> </speciesType>