Current definition of stoichiometry and role of ReactionElement inconclusive

[haeussma]

Currently, the role and the stoichiometry of an RectionElement is implicitly defined through the stochiometry field. This is ambiguous, since to express that the element is the a substrate one would define stoichiometry = -1 without knowing if the stoichiometry of the substrate truly is 1.

Thus, I recommend adding an additional enum field role (type ReactionRole) to the ReactionElement object.
The ReactionRole contains enums for substrate and product.

[JR-1991]

Wouldn't it be easier to roll back to explicit arrays for products and reactants?

[haeussma]

Like this:

Reaction

The Reaction object represents a chemical or enzymatic reaction and holds the different species and modifiers that are part of the reaction.

• id: Identifier
  • Description: Unique identifier of the reaction.
  • Term: schema:identifier
• name: string
  • Description: Name of the reaction.
• reversible: boolean
  • Description: Whether the reaction is reversible or irreversible. Default is False.
  • Default: False
• substrates: ReactionElement[]
  • Description: Substrates of the Reaction
• products: ReactionElement[]
  • Description: Products of the Reaction
• modifiers: Identifier[]
  • Description: List of species ids that are not consumed or build-up but influence the reaction.
• kinetic_law: Equation
  • Description: Mathematical expression of the reaction.
• species: ReactionElement[]
  • Description: List of reaction elements that are part of the reaction.

ReactionElement

• species_id: str
  • Description: Identifier of the species.
  • Term: schema:identifier
• stoichiometry: float
  • Description: Stoichiometry of the species within the reaction.

[JR-1991]

Fixed in #25