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[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: Sat, 31 Mar 2007 14:09:52 +1200
Hi Nicolas,

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.
>
> I think this is where the misundersting is. I thought you had a
> problem with the use of URIs, while you have a problem with the
> qualifier.

I misunderstand the scope of the property isDescribedBy. I also don't
think reverse engineering URIs to obtain meaning is a good practice.
How do you say one URI means the same as another if the URI scheme
changes? It seems you leave this up to the developer to make sure they
accomodate both instead of letting rdfs take care of this.

>
> > What do you mean by hardcode it in your language?
>
> If you create an element <bqs:PubMed_id> in your language, rather than
> having a generic reference scheme, with a type PubMed defined elsewhere.
>

I don't see what hardcoded means. Using properties that are defined in
a shared schema or standard is a pretty basic premise of sharing
information using RDF. How do you think RSS or dublin core works?
(http://purl.org/rss/1.0/schema.rdf is a useful read - here at least
you see the binding of a URI to a property declaration where that
property declaration has an intended meaning). All you need to do is
declare equivalence between predicates (which you can do using
property classes and property subclasses) and you are able to take
into account other forms for the same intended meaning. Note there is
also the "rdfs:isDefinedBy rdfs:subPropertyOf rdfs:seeAlso" definition
in RDFS. But that is different from equivalence per se.

our bqs namespace reflects OMG's Bibliographic Query Service
specification - see http://www.omg.org/docs/dtc/01-04-05.pdf

see also the attached RDF schema that Autumn Cuellar (from CellML)
developed for this.

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

What does generic mean? Standardised and used by everyone like a
published schema would be?

> >
> > What do you mean by the 'type' of metadata?
>
> EC page, PubMed entry, DOI indexed document, UniProt entry, Gene
> Ontology term etc.

The type of metadata is externalized as soon as it is presented in a
Schema and made public and adopted by the community.

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

are you meaning is-a relation? as in Type?

> It does not tell anything about the
> component to be annotated, or the resource used to annotate it. It
> describe the relationships between the concept represented by the
> component and the concept or object represented by the resource. It is
> similar to the Dublic-core isVersionOf, hasVersion etc.

I don't see this at all. isVersionOf and hasVersion is about
"versions" as in successors where both subject and object of the
relation are talking about the same thing in the same format but
differ somewhat in the content - e.g. a newer SBML file. Here is a
paste of what dublin core say:

isVersionOf

Label: Is Version Of

Term description: The described resource is a version, edition, or
adaptation of the referenced resource. Changes in version imply
substantive changes in content rather than differences in format.

Guidelines for creation of content:

Use only in cases where the relationship expressed is at the content
level. Relationships need not be close for the relationship to be
relevant. "West Side Story" is a version of "Romeo and Juliet" and
that may be important enough in the context of the resource
description to be expressed using isVersionOf. The Broadway Show and
the movie of "West Side Story" also relate at a similar level, but the
video and DVD of the movie are more usefully expressed at the level of
format, the content being essentially the same.

See also isFormatOf.

hasVersion

Label: Has Version

Term description: The described resource is a version, edition, or
adaptation of the referenced resource. Changes in version imply
substantive changes in content rather than differences in format.

Guidelines for creation of content:

See isVersionOf for basic guidelines.


>
> In the initial annotation scheme, we used only dc:relation. Then we
> decided to enrich the relationships by using the dcterms. But 1) they
> were too limited, 2) their semantics was slightly different
> (dcterm:hasPart really meant that the annotated document was
> physically composed of the parts pointed to).

Yes, dublin core is about the authoring and lifetime of a piece of
content. So yes, much of it applies to SBML and CellML models, but
using it to bind it to a Uniprot accession number or Gene Ontology
terms is outside it's scope I believe. Which I think you point out
when you say "their semantics was slightly different".

Why wouldn't the dublincore references and isReferencedBy be a useful
substitute for isDescribedBy when you are referring to a publication?
>From the dublin core spec:

"The isReferencedBy and References refinements enable the expression
of relationships that aid the user but are not necessary tied to the
life cycle or necessary for the intended use of the resource. This
relationship might be used to link an article critical of a resource
to that resource, a satire of a speech to the original speech, etc."

Surely that provides some semantic value?

cheers
Matt


>
> --
> 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
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>
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