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Definition of the species types and their state features

In order to build multi-component multistate entities, one needs to define the building blocks that will be combined. A given type of component, a SpeciesType, can carry several StateFeatures, which are multi-valued characteristics of the component. One can also specify if instances of a SpeciesType can act as binding sites. Apart from a unique identifier, a name, and several annotations, it is furthermore possible to define state features of a component, and the values taken by those state features. The following UML diagram shows how the structure of the SpeciesType looks like.


SpeciesType and all its associated classes.
SpeciesType and all its associated classes.


Contents

SpeciesType

The element SpeciesType, which is part of SBML Level 2 Version 4 specification, is not part of SBML Level 3 Version 1 any more. Instead, it will be defined in the multi package. The SpeciesType element carries not only the basic attributes which it had in SBML Level 2 Version 4 ( metaid , id , name ), but is also extended for the needs of describing multi-component entities with the attribute bindingSite and for the needs of multistate entities by linking it to a list of StateFeatures.

Definition of SpeciesType and its relation with SBase.
Definition of SpeciesType and its relation with SBase.

A species type can be used to describe a component of a supra-macromolecular assembly, but also a domain of a macromolecule. Such a domain can be a portion of the macromolecule, a non-connex set of atoms forming a functional domain, or just a conceptual construct suiting the needs of the modeler. The type of component can be specified by referring terms from the subbranch functional entity of the Systems Biology Ontology (http://biomodels.net/sbo/, [7]) through the optional sboTerm attribute. The following table provides typical examples of components or domains, but the list is absolutely not complete.


SBO identifier definition
SBO:0000242 channel
SBO:0000244 receptor
SBO:0000284 transporter
SBO:0000280 ligand
SBO:0000493 functional domain
SBO:0000494 binding site
SBO:0000495 catalytic site
SBO:0000496 transmembrane domain


The example below encodes a species type representing a ligand-gated ion channel, that is a transmembrane macromolecule that can form a ionic channel stabilised by the binding of ligands. Notice the notes and annotation that belong to the namespace of SBML Level 3 Version 1 core.

<multi:speciesType
       xmlns:core="http://www.sbml.org/sbml/level3/version1"
       xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1"
       xmlns:xhtml="http://www.w3.org/1999/xhtml"
       xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
       xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
       multi:id="speciesType1"
       multi:name="LGIC"
       multi:bindingSite="false"
       multi:sboTerm="SBO:0000242">
  <core:notes>
    <xhtml:body>
      <xhtml:p>LGIC is a Ligand-Gated Ion Channel</xhtml:p>
    </xhtml:body>
  </core:notes>
  <core:annotation>
    <rdf:RDF>
      <rdf:Description rdf:about="#_000003">
        <bqbiol:isVersionOf>
          <rdf:Bag>
            <rdf:li rdf:resource="urn:miriam:interpro:IPR002394"/>
          </rdf:Bag>
        </bqbiol:isVersionOf>
      </rdf:Description>
    </rdf:RDF>
  </core:annotation>
  <multi:listOfStateFeatures>
    <!-- some state features -->
  </multi:listOfStateFeatures>
</multi:speciesType>


The example below encodes a species type representing the binding site for a ligand, that could be used for instance in conjunction with the previous example.

<multi:speciesType 
       xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1"
       multi:id="speciesType2"
       multi:name="AgonistSite"
       multi:bindingSite="true"
       multi:sboTerm="SBO:0000494" />

StateFeature

A species type can carry any number of state features, which are characteristic properties specific for this type of species. The element StateFeature of SBML Level 3 Version 1 multi Version 1 corresponds to the "state variable" of the SBGN Entity Relationship language. A StateFeature is identified by an id and an optional name. A StateFeature is linked to a list of PossibleValues.

Definition of StateFeature and its relation with SBase.
Definition of StateFeature and its relation with SBase.

As all elements derived from SBase, StateFeature can link to Notes and Annotation, and carry a metaid , and an sboTerm . The value SBO:0000497 of sboTerm used in the example below corresponds to a "ternary switch".

<multi:stateFeature 
       xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1"
       multi:id="stateFeature1"
       multi:name="pore"
       multi:sboTerm="SBO:0000497">
  <multi:listOfPossibleValues>
    <!-- some possible values -->
  </multi:listOfPossibleValues>
</multi:stateFeature>

PossibleValue

Each state feature also requires the definition of all the possible values it can take. Those values will be used within a selector, to define the states an entity is allowed to take. A state feature is not obligatory a boolean property, but can carry any number of PossibleValue. A PossibleValue is identified by an id and an optional name .

Definition of PossibleValue and its relation with SBase.
Definition of PossibleValue and its relation with SBase.

As all elements derived from SBase, PossibleValue can link to Notes and Annotation, and carry a metaid , and an sboTerm . The sboTerm used in the example below corresponds to a "ternary switch".

<multi:possibleValue 
       xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1"
       multi:id="possibleValue1"
       multi:name="open"
       multi:sboTerm="0000416" />

Complete examples of use


<multi:speciesType 
       xmlns:core="http://www.sbml.org/sbml/level3/version1"
       xmlns:multi="http://www.sbml.org/sbml/level3/version1/multi/version1"
       xmlns:xhtml="http://www.w3.org/1999/xhtml"
       xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
       xmlns:bqbiol="http://biomodels.net/biology-qualifiers/"
       multi:id="speciesType1"
       multi:bindingSite="false"
       multi:name="LGIC"
       multi:sboTerm="SBO:0000242">
  <core:notes>
    <xhtml:body>
      <xhtml:p>
        LGIC is a Ligand-Gated Ion Channel. It contains a pore that can be open or closed.
      </xhtml:p>
    </xhtml:body>
  </core:notes>
  <core:annotation>
    <rdf:RDF>
      <rdf:Description rdf:about="#_000003">
        <bqbiol:isVersionOf>
          <rdf:Bag>
            <rdf:li rdf:resource="urn:miriam:interpro:IPR002394"/>
          </rdf:Bag>
        </bqbiol:isVersionOf>
      </rdf:Description>
    </rdf:RDF>
  </core:annotation>
  <multi:listOfStateFeatures>
    <multi:stateFeature 
           multi:id="stateFeature1"
           multi:name="pore"
           multi:sboTerm="SBO:0000497">
      <multi:listOfPossibleValues>
        <multi:possibleValue 
               id="possibleValue1"
               multi:name="open"
               multi:sboTerm="SBO:0000416" />
        <multi:possibleValue 
               id="possibleValue2"
               multi:name="closed"
               multi:sboTerm="SBO:0000417" />         
        <multi:possibleValue 
               id="possibleValue3"
               multi:name="desensitised"
               multi:sboTerm="SBO:0000417" />
      </multi:listOfPossibleValues>
    </multi:stateFeature>
  </multi:listOfStateFeatures>
</multi:speciesType>


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