(regardless of whether it’s inside a SpeciesReference or ModifierSpeciesReference object) exists in
(whether or not it can be inside a SpeciesReference or ModifierSpeciesReference object) exists within the worldwide namespace with the model, as described in Section three.3. The idand nameattributes has to be utilised as described in Section three.three. The speciesattribute: The SimpleSpeciesReference object class has a needed attribute, species, of variety SId. As together with the other attributes, it really is inherited by SpeciesReference and ModifierSpeciesReference. The worth of speciesmust be the identifier of a species defined inside the enclosing Model. The species is thereby declared as participating in the reaction getting defined. The precise function of that species as a reactant, item, or modifier within the reaction is determined by the subtype of SimpleSpeciesReference (i.e either SpeciesReference or ModifierSpeciesReference) in which the identifier appears. The sboTermattribute: The class SimpleSpeciesReference inherits from SBase the optional sboTermattribute of sort SBOTerm(see Sections 3..9 and 5). This implies that the object classes derived from SimpleSpeciesReference, namely SpeciesReference and ModifierSpeciesReference, all have sboTermattributes. When a worth is given to this attribute, it ought to be a valid SBO identifier referring to a MK-8742 participant function. The suitable SBO term is determined by whether or not the object is often a reactant, product or modifier. If a reactant, then it need to be a term inside the SBO:000000, “reactant” subbranch; if a item, then it ought to be a term inside the SBO:00000, “product” subbranch; and if a modifier, then it must be a term within the SBO:000009, “modifier” subbranch. The SpeciesReference and ModifierSpeciesReference situations really should have an “is a” partnership towards the term identified by the SBO identifier. The SBO terms chosen ought to be one of the most precise (narrow) one particular that defines the role with 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 solution term can only be assigned towards the sboTermattribute of a SpeciesReference instance when that instance is contained within the list of goods inside the containing Reaction instance. four.3.three SpeciesReferenceThe Reaction object class delivers a way to express which species act as reactants and which species act as solutions in a reaction. Inside a offered reaction, references to these species acting as reactants andor solutions are made employing instances of SpeciesReference objects in Reaction’s lists of reactants and solutions. The SpeciesReference structure inherits the mandatory attribute speciesand optional attributes id, name, and sboTerm, from the parent variety SimpleSpeciesReference; see Section four.3.2 for their definitions. It also defines attribute stoichiometryand element stoichiometryMath, described under.Author Manuscript Author Manuscript Author Manuscript Author ManuscriptJ Integr Bioinform. Author manuscript; readily available in PMC 207 June 02.Hucka et al.PageThe speciesattribute PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/23814047 worth has to be the identifier of an current species defined within the enclosing Model; the species is thereby designated as a reactant or item within the reaction. Which one it truly is (i.e reactant or product) is indicated by no matter whether the SpeciesReference seems inside the Reaction’s reactantor productlists. The stoichiometryattribute and stoichiometryMathelement: Item and reactant stoichiometries can be specified employing either stoichiometryor stoichiometryMathin a SpeciesReference object.
