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PM> What Robert mentioned earlier is that what we call
PM> "species" should be called "pool" because it is a
PM> specific subset of a chemical species in a model. What
PM> we now call species type is actually what the chemical
PM> species is. Our current practice is to add all unique
PM> chemical species as species types and annotate these
PM> with the appropriate MIRIAM rdf that points to the
PM> authoritative database entry for that chemical
PM> species. After this, we can infer that some "species"
PM> is also of that composition (because it is tagged with
PM> that species type).

Yes, yes, I agree, and what you wrote above actually
supports what I'm trying to say and what Nicolas already
explained several times in response to others: a species
type object *by itself* (in the absence of annotations)
doesn't give you semantics -- it's by virtue of annotations
that it gains meaning.

PM> Indeed, but it can be added with <annotation> and at
PM> that point it allows us to find out which "species"
PM> are of this chemical nature. (BTW this same mechanism
PM> could be used to group cell types too, etc. as long as
PM> the <annotation> is to the appropriate URN). Also, an
PM> SBO term can be added to indicate that this is a
PM> "simple molecule" (another problematic label, but I
PM> won't go there), or a protein, or a cell type (if/when
PM> we create the appropriate SBO term for that),
PM> etc. etc.

That's exactly what the SBML scheme is meant to support.

At least some of the confusion manifested in this discussion
thread seems to surround the idea that a species type object
provides meaning/semantics that the species object does not.
By itself it doesn't. The id or name doesn't have *meaning*
except maybe to human readers (and that's a bad assumption).
The species type object only provides a place onto which to
attach meaning, and a way to indicate grouping as you
describe below:

PM> The connections created by speciesType (or groups) are
PM> important as they carry the semantic meaning that
PM> these entities all have something in common. The
PM> something in common is what is pointed by the MIRIAM
PM> annotation on the speciesType/group level.

Yes.

And so, the real question is (as Lucian and Nicolas said in
separate messages) whether to include the capability in Core
or let it be a package.

MH

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