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> You will always need to pull apart the 'URI' (table2 MIRIAM document)
> to retrieve the datatype and identifier.

Well, yes you have to recognise what belongs to the data-type and what
belong to the identifier. But you do that all the time in RDF anyway. And
beside, we do it for you and can return one or more URLs.

> I guess I'm not sure why it isn't easier to keep the meaning of
> datatype and identifier seperate within the language context you are
> using - which is basically RDF. So that instead you would have
> something like:
>
> $X $QUALIFIER $DATATYPEINSTANCE
>
> $DATATYPEINSTANCE isA $DATATYPE
> $DATATYPEINSTANCE hasIdentifier $IDENTIFIER
> $DATATYPEINSTANCE hasPhysicalUrl $URL

Something like:

species calmodulin is calmodulin_in_uniprot
calmodulin_in_uniprot isA UniProt_entry
calmodulin_in_uniprot hasIdentifier P62158
calmodulin_in_uniprot hasPhysicalUrl http://www.ebi.uniprot.org/entry/P62158

- One cannot recognize "UniProt_entry" if it is a free string? This is why
there are MIRIAM data-types

- The physical URL being not stable, one cannot store actual URLs in the
models themselves.

So we are down to:

species calmodulin is calmodulin_in_uniprot
calmodulin_in_uniprot isA http://www.uniprot.org/
calmodulin_in_uniprot hasIdentifier P62158

How is-it different (in term of information content and of computing steps
necessary to parse) from:

species calmodulin is http://www.uniprot.org/#P62158

>> We do not need to relate them to specify that they all deal with
>> publications. It is already done by the bqmodel:isDescribedBy
>
> No, isDescribedBy has no semantic meaning - there is nothing to say
> that it explicitly defines a publication in a journal article or a
> vocabulary term.

Of course not, because we do not want to restrict the type of data used to
describe the component. This is what I said just above. What do-you mean
by
"isDescribedBy has no semantic meaning".

isDescribedBy exactly means the "is described by". How is that not a meaning?

What comes after the "by" can be a journal article, a webpage, a song, a
poem, a control vocabulary term, or a telepathic transmission.

> So there is no way to determine if some set of URIs are controlled
> vocab terms and some set are journal articles and some set are
> experimental result sets?

No. It is up to the user to decide what to do with what. See my ChEBI
example before. For some people ChEBI is a controlled vocabulary, for some
it is a database of chemical compound. For me, CAS is a database of
chemical compound, for CellML, it is a bibliographic resource.


--
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 at hotmail.com

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• [cellml-discussion] Biological and other non-model citations in CellML metadata?, Matt , 04/01/2007
  • [cellml-discussion] Biological and other non-model citations in CellML metadata?, Nicolas Le Novere, 04/01/2007
    • [cellml-discussion] Biological and other non-model citations in CellML metadata?, Matt , 04/03/2007
      • [cellml-discussion] Biological and other non-model citations in CellML metadata?, Nicolas Le Novere, 04/03/2007
        • [cellml-discussion] Biological and other non-model citations in CellML metadata?, Matt , 04/03/2007

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