First login?
Lost password?
 
 
cellml-discussion AT lists.cellml.org 
CellML Discussion List

Text archives Help


[cellml-discussion] Biological and other non-model citations in CellML metadata?


Chronological Thread 
  • From: matt.halstead at auckland.ac.nz (Matt )
  • Subject: [cellml-discussion] Biological and other non-model citations in CellML metadata?
  • Date: Fri, 30 Mar 2007 22:46:36 +1200
On 3/30/07, Nicolas Le Novere <lenov at ebi.ac.uk> wrote:
> On Fri, 30 Mar 2007, Matt wrote:
>
> > In those cases, for example bqs, where the object of the reference is
> > indeterminate or not of interest, it would be helpful to be able to
> > filter metadata without having to have knowledge of the values (in
> > this case reference URI schemes or identifiers) to determine the type
> > of metadata property you are dealing with.
>
> How do-you do that? How do-you decrypt a foreign language without a
> dictionary?

You have typed properties, for example you simply pass over everything
that is a bqs:reference because you are not interested in it. You
don't need to know anything about the schema restrictions underlying
objects of bqs:reference to dertermine that this is a bqs:reference.

With isDescribedBy being used generally for all kinds of external
references, you have no way of knowing what the intention of the
instance of this relation without inspecting the object value, and to
do that you need to understand all current and future kinds of data
that could be used.

>
> > Are you suggesting every processor of SBML metadata need to iterate
> > over all isDescribedBy predicates and evaluate the objects of these
> > and reverse engineer these back into some knowledge of what kind of
> > description this is?
>
> Yes. There are no alternative as far as I know. Either you hard-code
> the type of description in your language, or you externalise it. In
> both case, you have to go through a look-up table.

What do you mean by hardcode it in your language?

>
> The big advantage of externalising the type of metadata is that the
> scheme is generic.

What do you mean by the 'type' of metadata?

> You do not need to know what the metadata is when
> you parse the file. You can if you wish. For instance, MIRIAM resource
> only provide the syntax of hyperlinks at the moment. We can imagine a
> case where you would like to access a resource programmatically and
> download some data, e.g. 3D coordinates from the PDB. In that case you
> would encode a specific processing in your code.

But it would seem that you could use isDescribedBy for this since it
doesn't seem limited to pointing to any specific kind of value.

>
> But maybe I am actually misunderstanding the problem.

I think more I am misunderstanding the range of use isDescribedBy is ok for.

>
> --
> 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
>

cheers
Matt


Archive powered by MHonArc 2.6.18.

Top of page