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> As far as I can see, any argument you wage against species type or
> entity could just as well be used against having compartment as an
> attribute.

Of course not. A compartment is an essential component of a species. And
its identifier carries a precise semantics that is translated in
mathematical expressions by the values of its size.

> Also, can you please explain how you would unambiguously annotate
> that two species refer to the same phospho-state of a protein? Or the
> same mutant? Or the same dimer?

But that has nothing to do with the current debate. A free-form identifier
will not address that. If you want to do that with no annotations, you can
create a group, e.g. "MAPK-122P", and attach to it an element notes where
you describe in human readable terms what it is.

Controlled annotations currently have a limited semantics. At the moment
we can only say that a species is a version of a protein, and that a
species is phosphorylated. We actually know how we could say it is a
phosphorylated version of a protein. This requires to put an id on an
annotation. It was refused for L2V4 and postponed to L3, but finally did
not make it to the core.

But again, this is not the current issue. The current issue is to tag
several species as being versions of the same class of species. This is
perfectly achieved with the groups.

THAT SAID, SpeciesType is not going to disappear. It is a core part of the
multi package.


--
Nicolas LE NOVERE, Computational Neurobiology,
EMBL-EBI, Wellcome-Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
Tel: +44(0)1223494521, Fax: +44(0)1223494468, Mob: +44(0)7833147074
http://www.ebi.ac.uk/~lenov, AIM:nlenovere, MSN:nlenovere@hotmail.com

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