RDF Schema (was: [Biocorba-l] Annotations)

[Juha Muilu]

Thomas Down wrote:
> 
> On Wed, Jun 06, 2001 at 10:46:48AM +0100, Juha Muilu wrote:
> > Thomas Down wrote:

Thanks for correcting this! I was on wrong tracks

> 
> My vision of the schema mechanism is just to use it to
> define the types of annotations that you might expect to
> find associated with a given type of bio-entity (sequence,
> feature, whatever).  Potentially (and this is the really
> exciting bit, in some ways) we can also use the same kinds
> of mechanism to link into ontologies which define the
> relationships between the entity and it's annotations

Sounds interesting... but I do not quite follow... Could you give an
example how you implement it (i.e. twist it from iron wire)

The metadata which describes the schema is an another resource
associated with the annotation or something...?

> (and hence make it easier to interwork and query annotated
> data from different sources).
> 
> The basic RDF mechanism is a set of triples looking like:
> 
>     resource_a    --------------------->   resource_b
>                       predicate
> 
> You can look at this relationship as definining some kind
> of `property' of resource_a.
> 
> This model is compatible with BioJava Annotations, and the
> AnnotationHolder stuff in your IDL.  The annotated entity
> (Annotatable, to use the BioJava terminology) is resource_a,
> the annotation key is the predicate, and the annotation
> value is resource_b (or perhaps a pointer to resource_b --
> a URI, for instance).
> 
> RDF Schema and DAML (I need to re-read some specifications
> to get the division between these two clearer -- I'm more
> familiar with DAML, which builds upon and extends RDF Schema)
> give mechanisms to define the set of properties you would
> expect a given type of resource to have.
> 
> Retrofitting into current interfaces:
> 
> My point about this was mainly that the current interfaces
> model data that can be looked at in the RDF model, and can
> hence be described using and RDF schema.  The way I see things
> going:
> 
>   - Simple object model to describe the schemas.

Perhaps the we can also have some kind of validation services,  which
uses the schema to validate the data? 

> 
>   - Add one extra property on Annotation (or perhaps Annotatable)
>     which links into the schema model.

Can it be just that named resource? So no explicit method is needed to
get reference to the schema model


> 
> > How does all this relate to the DAS ?
> 
> [Maybe not quite the target topic for this list, but it's an
> interesting question, and I think relevant, so...]
> 
> Currently, the types of data that can be communicated in DAS
> are rather restricted, and are defined entirely by the DAS
> specification.  Basically just `coloured-box' features and
> links out to web pages.
> 
> I'm looking to see a richer DAS.  We're currently looking at
> the XFF feature table format:
> 
>   http://www.biojava.org/thomasd/XFF/
> 
> as a cornerstone for the next generation of DAS.  If you look
> at this, it has `strongly typed' core feature data structures.
> To these, you can add `detail' elements (weakly bound data).
> Once again, the relationship between a feature and it's details
> can be looked at as an RDF triple.  This means we can link
> schemas in, just as above.  Which could become particularly
> important when we start building clients with GUI interfaces
> for querying the DAS.

Do the details corresponds to qualifiers we have? I think that original
purpose to have those in the BSA was to be able to add extra annotations
to annotations. 

This something we must keep align

> 
> In the DAS/1.9xx there's also an extra concept of annotations
> services, which offer extra information about a given feature
> (e.g. if there is a features service offering a set of gene
> predictions, somebody else could set up an annotations service
> which adds links from the `gene' features to PDB structures of
> gene products [where known].  Or expression profiles.  Or functional
> annotation.  Or anything, really).  The current plan is that
> elements from an annotations service are treated equivalently
> to details elements embedded into the original feature table.
> 
> [This is all quite new at the moment, and really needs some testing
> and experimentation.  I've got a design for
> a prototype implementation, and will hopefully get it implemented
> over the next couple of weeks.]
> 
> Anyone else interested in this?

Good work. I am interested :-) Need some time to understand this
properly, though

> 
>   Thomas.
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