Le in PMC 207 June 02.Hucka et al.Pagemathematical interpretation. Simulators and
Le in PMC 207 June 02.Hucka et al.Pagemathematical interpretation. Simulators and other numerical analysis application may well ignore CompartmentType objects and references to them in a model. There is no mechanism in SBML for representing hierarchies of compartment forms. One CompartmentType object instance can’t be the subtype of one more CompartmentType object; SBML Orexin 2 Receptor Agonist custom synthesis offers no means of defining such relationships. four.five. The id and name attributesAs with other important class of objects in SBML, CompartmentType includes a mandatory attribute, id, applied to offer the compartment form an identifier. The identifier should be a text string conforming for the syntax permitted by the SId information type described in Section three..7. CompartmentType also has an optional name attribute, of form string. The name and id attributes have to be utilized as described in Section three.3. 4.5.two The sboTerm attributeCompartmentType inherits an optional sboTerm attribute of kind SBOTerm from its parent class SBase (see Sections 3..9 and five). When a value is given to this attribute within a CompartmentType instance, the worth really should be an SBO identifier referring to a material entity (i.e terms derived from SBO:0000240, “material entity”). The connection is from the type “the compartment variety is really a X”, exactly where X will be the SBO term. The term selected need to be probably the most precise (narrow) one particular that captures the part with the compartment type in the model. four.5.3 ExamplesThe following partial SBML instance illustrates a compartment sort applied to relate together many individual compartments inside a hypothetical model.Author Manuscript Author Manuscript Author Manuscript Author Manuscript4.six Species types The term species variety refers to reacting entities independent of location. These incorporate easy ions (e.g protons, calcium), straightforward molecules (e.g glucose, ATP), substantial molecules (e.g RNA, polysaccharides, and proteins), and other folks. The SpeciesType object class is intended to represent these entities. Its definition is shown in Figure four. SpeciesType objects are included in SBML to enable Species (Section 4.8) from the same form to be associated together. It is actually a conceptual construct; the existence of SpeciesType objects in a model has no effect on the model’s numerical interpretation. Except for the requirement for uniqueness of speciesspecies type combinations situated in compartments (described in Section 4.eight.2), simulators as well as other numerical analysis computer software could PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/23637907 ignore SpeciesType structures and references to them in a model.J Integr Bioinform. Author manuscript; obtainable in PMC 207 June 02.Hucka et al.PageThere is no mechanism in SBML for representing hierarchies of species sorts. 1 SpeciesType object instance cannot be the subtype of another SpeciesType; SBML supplies no indicates of defining such relationships. four.six. The id and name attributesAs with other significant object classes in SBML, SpeciesType includes a mandatory attribute, id, utilized to offer the species type an identifier. The identifier has to be a text string conforming to the syntax permitted by the SId data type described in Section 3..7. SpeciesType also has an optional name attribute, of sort string. The name and id attributes have to be utilized as described in Section three.three. four.6.2 The sboTerm attributeSpeciesType inherits an optional sboTerm attribute of kind SBOTerm from its parent class SBase (see Sections three..9 and five). When a value is given to this attribute in a SpeciesType instance, the worth need to be an SBO identifier referring to a material entity (i.e terms derived fro.
