(no matter if it is actually within a SpeciesReference or ModifierSpeciesReference object) exists in
(irrespective of whether it is inside a SpeciesReference or ModifierSpeciesReference object) exists within the worldwide namespace from the model, as described in Section three.three. The idand nameattributes have to be made use of as described in Section three.three. The speciesattribute: The SimpleSpeciesReference object class has a essential attribute, species, of sort SId. As with the other attributes, it can be inherited by SpeciesReference and ModifierSpeciesReference. The worth of speciesmust be the identifier of a MedChemExpress GSK583 species defined in the enclosing Model. The species is thereby declared as participating inside the reaction getting defined. The precise role of that species as a reactant, product, or modifier inside 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 three..9 and 5). This means that the object classes derived from SimpleSpeciesReference, namely SpeciesReference and ModifierSpeciesReference, all have sboTermattributes. When a value is provided to this attribute, it needs to be a valid SBO identifier referring to a participant part. The suitable SBO term is dependent upon whether or not the object is often a reactant, solution or modifier. If a reactant, then it need to be a term in the SBO:000000, “reactant” subbranch; if a solution, then it needs to be a term in the SBO:00000, “product” subbranch; and if a modifier, then it ought to be a term within the SBO:000009, “modifier” subbranch. The SpeciesReference and ModifierSpeciesReference instances must have an “is a” connection to the term identified by the SBO identifier. The SBO terms chosen ought to be essentially the most precise (narrow) one particular that defines the part in the species within the reaction. An SBO reactant term can only be assigned to 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 in the list of products in 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 goods within a reaction. Within a given reaction, references to these species acting as reactants andor products are created making use of 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 type SimpleSpeciesReference; see Section four.3.2 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; obtainable in PMC 207 June 02.Hucka et al.PageThe speciesattribute PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/23814047 value must be the identifier of an current species defined inside the enclosing Model; the species is thereby designated as a reactant or item within the reaction. Which one particular it’s (i.e reactant or solution) is indicated by whether or not the SpeciesReference seems in the Reaction’s reactantor productlists. The stoichiometryattribute and stoichiometryMathelement: Product and reactant stoichiometries can be specified using either stoichiometryor stoichiometryMathin a SpeciesReference object.
