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SpeciesType

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The element 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 StateFeatures, PossibleValues and BindingSites. The following UML diagram shows how the structure of the SpeciesType looks like.

Definition of classes SpeciesType, StateFeature, PossibleValue, and BindingSite, as well as the container classes ListOfStateFeatures, ListOfPossibleValues and ListOfBindingSites.
Definition of classes SpeciesType, StateFeature, PossibleValue, and BindingSite, as well as the container classes ListOfStateFeatures, ListOfPossibleValues and ListOfBindingSites.


StateFeature

A 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.

PossibleValue

Each 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 Reaction. 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>

BindingSite

In addition to StateFeatures, a 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 minOccur and 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>


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