SpeciesReference

SpeciesReference is a data element used in computational models of biochemical networks, most notably in the Systems Biology Markup Language (SBML). It represents a single participation of a chemical species in a reaction, indicating whether the species behaves as a reactant or a product. Each SpeciesReference points to a defined Species in the model by its identifier, ensuring consistency across the model. In a given reaction, multiple SpeciesReference entries appear in the appropriate list (reactants or products) to express the overall stoichiometry of the transformation.

Key attributes describe how a species participates in a reaction. The species attribute identifies the referenced Species. The stoichiometry attribute specifies the coefficient with which the species participates, typically a non-negative real number; the sign of the species’ influence on the reaction is determined by whether the reference is in the reactants list or the products list. An optional constant flag indicates whether the coefficient is treated as fixed during simulation. In SBML, the referenced Species must exist in the model, and the set of reactant references and product references together contribute to the reaction’s stoichiometry and to the construction of the model’s stoichiometric matrix.

Example: For the reaction A + 2B -> C, there would be a SpeciesReference for A in the reactants with stoichiometry 1, a SpeciesReference for B in the reactants with stoichiometry 2, and a SpeciesReference for C in the products with stoichiometry 1. This structure allows software tools to compute mass balances and to apply rate laws consistently across the modeled network.