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


Chronological Thread 
  • From: lenov at ebi.ac.uk (Nicolas Le Novere)
  • Subject: [cellml-discussion] Biological and other non-model citations in CellML metadata?
  • Date: Fri, 30 Mar 2007 09:10:09 +0100 (BST)
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?

> 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.

The big advantage of externalising the type of metadata is that the
scheme is generic. 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 maybe I am actually misunderstanding the problem.

--
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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