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Hello Mike, All,

On Sat, Sep 19, 2009 at 10:14 PM, Michael Hucka <mhucka@caltech.edu> wrote:
>  shoops> Unfortunately we must correct the specs as what
>  shoops> the specs says can not be encoded in RDF at least
>  shoops> not in the subset of RDF/XML we allow. I repeat
>  shoops> from the standpoint of the information containt in
>  shoops> RDF there is no difference.
>
> Stefan,
>
> I'm sorry, but I disagree.  My interpretation of the
> following constructs aligns with Nicolas Le Novere's and (I
> think) Oliver's:

Yes, it aligns. So far, I only commented on the meaning of the RDF,
because I was not sure whether SBML/MIRIAM specifications were as I
would expect. Thanks to your example, I can see they are exactly as I
would expect based on the meaning of the underlying RDF.

> Case 1:
> ------
>
> <rdf:description about ...>
>  qualifier
>    bag
>      A
>      B
> </rdf:description>
>
>
> Case 2:
> -------
>
> <rdf:description about ...>
>  qualifier
>    bag
>      A
>
>  qualifier
>    bag
>      B
> </rdf:description>
>
>
> By "qualifier", I mean the ones such as hasVersion, hasPart,
> etc.  An RDF bag lists a set of things that are
> simultaneously true, but in no particular order.  However,
> two separate instances of the same qualifier inside an
> rdf:description, containing different bags, do not collapse
> into a single qualifier-bag combination.
>
> This has been the interpretation for many years -- in fact,
> the SBML specification has the following example since L2v2
> (2006!):
>
>   <bqbiol:hasVersion>
>     <rdf:Bag>
>       <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A17345"/>
>       <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A17552"/>
>       <rdf:li rdf:resource="urn:miriam:obo.chebi:CHEBI%3A17627"/>
>     </rdf:Bag>
>   </bqbiol:hasVersion>
>   <bqbiol:hasVersion>
>     <rdf:Bag>
>       <rdf:li rdf:resource="urn:miriam:kegg.compound:C00035"/>
>       <rdf:li rdf:resource="urn:miriam:kegg.compound:C00044"/>
>       <rdf:li rdf:resource="urn:miriam:kegg.compound:C00144"/>
>     </rdf:Bag>
>   </bqbiol:hasVersion>
>
> We've been describing it this way for a long time.  See, for
> example, a presentation I did in 2007 (updated in 2008):
>
> http://www.ebi.ac.uk/compneur-srv/miriam/elements/MIRIAM-qualifiers-summary-2008-09-23.pdf

Yes, which would be in N3 something like:

:myMetaID bqbiol:hasVersion _:b1 .
_:b1 rdf:type rdf:bag .
_:b1 rdf:li <urn:miriam:obo.chebi:CHEBI%3A17345> .
_:b1 rdf:li <urn:miriam:obo.chebi:CHEBI%3A17552> .
_:b1 rdf:li <urn:miriam:obo.chebi:CHEBI%3A17627> .
:myMetaID bqbiol:hasVersion _:b2 .
_:b2 rdf:type rdf:bag .
_:b2 rdf:li <urn:miriam:kegg.compound:C00035> .
_:b2 rdf:li <urn:miriam:kegg.compound:C00044> .
_:b2 rdf:li <urn:miriam:kegg.compound:C00144> .

where :myMetaID is the meta id and b1 and b2 are two arbitrary
labels each for a blank node.

Take care
Oliver

--
Oliver Ruebenacker, Computational Cell Biologist
BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
Center for Cell Analysis and Modeling
http://www.oliver.curiousworld.org
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