(no matter if it truly is inside a SpeciesReference or ModifierSpeciesReference object) exists in
(no matter whether it truly is inside a SpeciesReference or ModifierSpeciesReference object) exists in the international namespace of your model, as described in Section 3.3. The idand nameattributes should be utilised as described in Section three.3. The speciesattribute: The SimpleSpeciesReference object class includes a necessary attribute, species, of type SId. As together with the other attributes, it can be inherited by SpeciesReference and ModifierSpeciesReference. The value of speciesmust be the identifier of a species defined inside the enclosing Model. The species is thereby declared as participating inside the reaction becoming defined. The precise part of that species as a reactant, solution, or modifier within the reaction is determined by the subtype of SimpleSpeciesReference (i.e either SpeciesReference or ModifierSpeciesReference) in which the identifier seems. The sboTermattribute: The class SimpleSpeciesReference inherits from SBase the optional sboTermattribute of kind SBOTerm(see Sections 3..9 and five). This means that the object classes derived from SimpleSpeciesReference, namely SpeciesReference and ModifierSpeciesReference, all have sboTermattributes. When a value is offered to this attribute, it ought to be a valid SBO identifier referring to a participant function. The suitable SBO term depends upon irrespective of whether the object can be a reactant, item or modifier. If a reactant, then it needs to be a term inside the SBO:000000, “reactant” subbranch; if a solution, then it ought to be a term within the SBO:00000, “product” subbranch; and if a modifier, then it should be a term in the SBO:000009, “modifier” subbranch. The SpeciesReference and ModifierSpeciesReference instances must have an “is a” partnership for the term identified by the SBO identifier. The SBO terms chosen ought to be probably the most precise (narrow) a single that defines the function of the species in the reaction. An SBO reactant term can only be assigned for the sboTermattribute of a SpeciesReference instance when that instance is contained in the list of reactants within the containing Reaction instance. Similarly, an SBO product term can only be assigned to the sboTermattribute of a SpeciesReference instance when that instance is contained inside the list of solutions inside the containing Reaction instance. four.three.three SpeciesReferenceThe Reaction object class gives a technique to express which species act as reactants and which species act as goods inside a reaction. Inside a provided reaction, references to these species acting as reactants andor solutions are created utilizing situations of SpeciesReference objects in Reaction’s lists of reactants and items. The SpeciesReference structure inherits the mandatory attribute speciesand optional attributes id, name, and sboTerm, from the parent variety SimpleSpeciesReference; see Section four.3.two for their definitions. In addition, it defines attribute stoichiometryand element stoichiometryMath, described below.Author Manuscript Author Manuscript Author Manuscript Author ManuscriptJ Integr Bioinform. Author manuscript; Potassium clavulanate:cellulose (1:1) site accessible in PMC 207 June 02.Hucka et al.PageThe speciesattribute PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/23814047 worth have to be the identifier of an current species defined within the enclosing Model; the species is thereby designated as a reactant or solution within the reaction. Which 1 it is actually (i.e reactant or item) is indicated by irrespective of whether the SpeciesReference seems inside the Reaction’s reactantor productlists. The stoichiometryattribute and stoichiometryMathelement: Product and reactant stoichiometries is often specified applying either stoichiometryor stoichiometryMathin a SpeciesReference object.