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Oliver Ruebenacker wrote:

> It surprises me that, after even Nicolas conceded the weakness of
> MIRIAM annotations, you still insist they are perfect and only
> "cumbersome".

I never "conceded" that those annotations could not be used to identified
species of the same "kind". I merely pointed out that they had a limited
expressibility. But there is nothing better except full-blown OWL. And this
problem is not specific to SBML. BioPAX cannot encode those things as well.
Describing the structure is better with BP L3, but without Alan
Ruttenberg's proposal (which is effectively BioPAX's MIRIAM annotations)
one cannot identify the entities. If you load a BioPAX file coming from a
resource and another from another resource, you will get disconnected
networks if the there is no agreement on an annotation scheme.

> If a species is a pool of indistinguishable things, it is only
> natural that two species that contain the same indistinguishable
> things have a unique relationship and therefore require a unique way
> of being grouped. Trying to use the same grouping scheme for
> distinguishable and indistinguishable things does not make sense.

But ... this is exactly what we do not do. Species are grouping
indistinguishable things. Groups are grouping sets of distinguishable things.

--
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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