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Overloading Semantics For SBML Objects By Type

Overloading semantics for SBML objects by type

Object type Overloadable Convergeant Overloadable Divergent Overloadable Semantics Comments
species yes no no flattened species has union of the species references incident to all the relevant species
reaction yes yes yes flattened reaction has only the species references incident to the overloading reaction
compartment yes no no
species type no no no should use inclusion instead - covers all elements taht are used to assemble a complex type
compartment type no no no should use inclusion instead
rule yes no no not clear how you will refer to a rule as they don't have an identity seperate from variable assigned
constraint no no no really don't want this to be overloadable as constraint will tell the user that the submodel is incorrect
event yes no no same issues as rule with identity
link no no no
instance yes no no the set of ports must match not really clear what happens when ports are bypassed
port yes no no linking constraints from this table are taken from original object (speciesPort acts as a species)

-- Andrew Finney, 10 Sep 2007

(Comment from Magdeburg): Convergent links should not be allowed in general. To allow for m to n m replacement of reactions, we propose to define a set of reactions and to link from this set to the reaction to be replaced.



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