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Oliver Ruebenacker wrote:
>>> 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.
>
> If size was the only issue, you could have that more easily and more
> flexibly by adding a size attribute to the species. Compartments would
> be an unjustified overkill.

No, no, no. We are talking about quantitative models here. 1) you need a
symbol for representing the compartment in equations and 2) you need to
enforce consistency so that the compartment of all the relevant species is
maintained at the same value.

SBML is not BioPAX and vice-versa (otherwise we would not need two
languages). In BioPAX, one is interested in the conceptual relationships
between entities. This is why compartment was, in L2, an attribute of a
physicalEntityParticipant. In SBML, the purpose is to encode models with
rules describing the evolution of the model.

>>> 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.
>
> Of course it has to do with the current debate. You brought up
> annotations as an argument against species types

No, I did not. I say that if you need to describe precisely biological
knowledge that does not affect the interpretation of the model, you must
use annotation.

The debate is (or should be) on how to group species in a larger set that
one can identify. The proposal of Robert was to use another label such
"phosphorylated_mapk", that would cover all the phosphorylated MAPK,
whether in the cytoplasm or the nucleus. This is different to encode in a
computationally usable framework the fact that this "species type"
represent the set of all proteins in the cell that have the same nucleotide
sequence and are phosphorylated.

> All we want is being able to say that two species within the same
> model are the same entity. You can do that perfectly with species
> types, even if they are called jack and jill.

And you already can with the name. And you will be able with the groups.

>> THAT SAID, SpeciesType is not going to disappear. It is a core part of the
>> multi package.
>
> We need to have entities in the SBML Core, not some package, because
> entities are essential to the semantics of SBML. As essential as
> compartments.

No, it is not. If you load an SBML file in a simulator, any simulator, with
or without specieTypes, and click run, you get exactly the same curves. If
you suppress the compartments, you cannot reconstruct the ODEs.

--
Nicolas LE NOVERE, Computational Neurobiology, EMBL-EBI, Wellcome-Trust
Genome Campus, Hinxton CB101SD UK, Mob:+447833147074, Tel:+441223494521
Fax:468,Skype:n.lenovere,AIM:nlenovere,MSN:nlenovere@hotmail.com(NOT email)
http://www.ebi.ac.uk/~lenov/, http://www.ebi.ac.uk/compneur/


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