(no matter if it’s Nanchangmycin site within a SpeciesReference or ModifierSpeciesReference object) exists in
(regardless of whether it is within a SpeciesReference or ModifierSpeciesReference object) exists inside the global namespace of your model, as described in Section three.3. The idand nameattributes must be made use of as described in Section three.three. The speciesattribute: The SimpleSpeciesReference object class features a expected attribute, species, of kind SId. As with all the other attributes, it is actually 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 within the reaction becoming defined. The precise role of that species as a reactant, solution, or modifier inside 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 type SBOTerm(see Sections 3..9 and 5). This suggests that the object classes derived from SimpleSpeciesReference, namely SpeciesReference and ModifierSpeciesReference, all have sboTermattributes. When a value is offered to this attribute, it needs to be a valid SBO identifier referring to a participant function. The proper SBO term will depend on regardless of whether the object is actually a reactant, item or modifier. If a reactant, then it really should be a term inside the SBO:000000, “reactant” subbranch; if a product, then it must be a term inside the SBO:00000, “product” subbranch; and if a modifier, then it ought to be a term inside the SBO:000009, “modifier” subbranch. The SpeciesReference and ModifierSpeciesReference situations must have an “is a” connection to the term identified by the SBO identifier. The SBO terms chosen should be probably the most precise (narrow) one particular that defines the part of your species within the reaction. An SBO reactant term can only be assigned for the sboTermattribute of a SpeciesReference instance when that instance is contained inside the list of reactants in 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 in the list of items inside the containing Reaction instance. four.3.three SpeciesReferenceThe Reaction object class provides a approach 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 goods are created working with instances of SpeciesReference objects in Reaction’s lists of reactants and merchandise. The SpeciesReference structure inherits the mandatory attribute speciesand optional attributes id, name, and sboTerm, in the parent type SimpleSpeciesReference; see Section four.3.two for their definitions. In addition, it defines attribute stoichiometryand element stoichiometryMath, described beneath.Author Manuscript Author Manuscript Author Manuscript Author ManuscriptJ Integr Bioinform. Author manuscript; out there 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 existing species defined within the enclosing Model; the species is thereby designated as a reactant or solution in the reaction. Which a single it truly is (i.e reactant or item) is indicated by no matter if the SpeciesReference appears in the Reaction’s reactantor productlists. The stoichiometryattribute and stoichiometryMathelement: Solution and reactant stoichiometries could be specified employing either stoichiometryor stoichiometryMathin a SpeciesReference object.