Forums

The topic of this vote is:
ADDING AN IDENTIFIER TO SimpleSpeciesReference

The URL for the voting page is:
http://www.surveymonkey.com/s.asp?u=508511613662

Additional background is available in the minutes from the
October SBML Forum meeting at
http://www.sbml.org/forums/index.php?t=msg&th=713&rid=2

The SBML Level 2 Version Specification is at:
http://sbml.org/wiki/sbml-level-2-version-2.pdf

Another proposed change to SBML in SBML Level 2 Version 2 is
the addition of an identifier to the SimpleSpeciesReference
structure in Reactions. SimpleSpeciesReference currently
lacks an identifier.

There have not been significant objections to the idea of
adding an identifier field to SimpleSpeciesReference.
However, in the October 2005 SBML Forum meeting, a question
arose about the best *scope* of such identifiers in
SimpleSpeciesReference objects. Should their scope be local
to a given Reaction object, or should their scope be global
to the whole model?

The argument for restricting the identifiers to have local
scope is based on the belief that the majority of references
to SimpleSpeciesReference objects or their derived objects
(SpeciesReference and ModifierSpeciesReference) will be
(especially in future extensions) coming from within the
enclosing Reaction object. One example concerns the complex
species extensions proposed for SBML Level 3. Here, the
SpeciesReference may represent a set of species through a
kind of template mechanism rather than by referring to a
specific species. In this case, the KineticLaw would need
to refer to the concentration of the entity and would use
the SpeciesReference identifier to do this. The
SpeciesReference identifier would only have meaning within
the context of the Reaction, and thus it's unnecessary and
redundant to require identifiers that are unique across the
whole model for these species references that only need to
be unique with the Reaction. (However, it must be
acknowledged that using global scoping for SpeciesReference
identifiers would also not *preclude* this application.)

The argument for having the identifier scope be global is
that there are situations where one needs to point to
SpeciesReference objects from outside their Reactions, and
in those cases, having unique identifiers leads to direct
and easier-to-implement references to SimpleSpeciesReference
or their derived objects from outside of Reactions. If the
scope of identifiers is local to a Reaction, then references
from *outside* the reactions would need to specify two
identifiers: (i) the identifier of the reaction PLUS (ii)
the identifier of the SimpleSpeciesReference. A concrete
example of where this would happen is with the SBML Layout
proposal. Graphical editing tools will need the ability to
manipulate the graphical objects (SpeciesReferenceGlyphs)
associated with SpeciesReferences. Although it would be
technically possible to use two identifiers in
SpeciesReferencesGlyphs to uniquely identify the
corresponding SpeciesReferences, this approach (1) would run
counter to almost all other examples of references in SBML,
which require only one identifier, and (2) would involve
connecting globally-scoped SpeciesReferenceGlyphs
identifiers with locally-scoped SpeciesReference
identifiers, which seems unnecessarily confusing and
error-prone. Those who favor global scoping of
SimpleSpeciesReference identifiers argue that these costs
are not outweighed by the benefits of local scoping.

Do you feel the scope of the identifiers should be local to
a given Reaction object, or global to the whole model?

Please cast your vote by using the voting page at
http://www.surveymonkey.com/s.asp?u=508511613662

Andrew and Mike