Chronological Thread 

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On 4/3/07, Nicolas Le Novere <lenov at ebi.ac.uk> wrote:
> > 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.

In what part of RDF is this done?

>
> > 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.

Nope. I should be clearer about what would be published globally and
what should be in a particular model.

Published globally:

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

UniProt_entry subClassOf DatabaseRecord (that's quite generic)
hasUniprotEntry subPropertyOf hasDatabaseRecord
hasDatabaseRecord subPropertyOf isDescribedBy

In the model:

x hasUniProtEntry calmodulin_in_uniprot


Now one can filter all annotations in a model for database links only,
or uniprot links only etc. It all just works when using RDF Schema.


>
> 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
>

For the reason's I give above.

> >> 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?

In the RDF world you have not attributed any meaning. It could be used
for anything.


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

Right, and so if it can be followed by anything then it has no meaning
.... there is nothing to distinguish it from any property that someone
may make up.

>
> > 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.

But when a person uses it, they will have a context. It may be one or
more of those from your list, but it is still useful for them to
restrict the intention of the property to something close to what they
mean. I don't particularly want to guess whether someone is intending
the DataType to mean 'chemical compound' as opposed to 'bibliographic
resource'. For all I know the record that I may be able to locate
based on this URI might have value in both domains and I would want to
know what they were intending. Of course you'd hope the record was RDF
anyway and you were able to point to the record attribute by a full
URI.

>
>
> --
> 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
>
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion
>

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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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