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[cellml-discussion] Time for a decent RDF library in the CellML API?


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  • From: matt.halstead at auckland.ac.nz (Matt)
  • Subject: [cellml-discussion] Time for a decent RDF library in the CellML API?
  • Date: Wed, 6 Sep 2006 16:31:22 +1200
The fact there is no standardized API does not mean we invent our
own. There are plenty of RDF implementations around and a huge amount
of overlap between them. I suggest we find that subset that shows
reasonable intersection over the most popular rdf libraries and use
that. But in saying that, I'm not sure you need to be exposing the
RDF through an RDF centric API. The developers of the metadata editor
found it more useful to offer an API that was centered around the
kinds of metadata that needed to be supplied - for instance to add a
series of authors, it was much nicer to be able to populate an
authors data structure, especially since in the cellml metadata
specification there is a strict interpretation of the underlying RDF
data structures - such as bags, lists etc.

There is nothing stopping anyone adding arbitrary RDF using whatever
RDF tool they want.

Specifying and implementing our own RDF API does not make sense to me
at all.

cheers
Matt


On 6/09/2006, at 1:44 PM, Andrew Miller wrote:

> Hi all,
>
> The CellML API currently provides two ways to access RDF for the
> model:
> 1) As a single serialised chunk, or
> 2) As a DOM node for the RDF:Description
>
> Neither of these approaches are very good, because RDF/XML can be
> spread
> throughout the model, and so you don't know that you have put all the
> triples you want into a local RDF library if you need to perform any
> manipulations on it. They also make it very hard to change the RDF/XML
> in the model (removing it and putting it back through DOM operations
> might not be easy if the structure of the XML has changed).
>
> There is currently no widely accepted standard API, so I propose
> that we
> adopt our own, taking into consideration the designs used in Mozilla
> (http://lxr.mozilla.org/seamonkey/source/rdf/base/idl/) and Jena (and
> also the other RDF libraries available). At this stage, I think that
> supporting query languages would add too much complexity, so we should
> probably stick to basic operations like:
>
> 1) Given a subject and predicate, fetching the object. Also
> fetching the
> subject from object and predicate.
> 2) Given a subject, fetch all known predicates. Likewise for object.
> 3) Given a predicate, fetch all known subject / object pairs (perhaps.
> This might be expensive in some implementations).
> 4) Given a subject, predicate, and object, make an assertion.
> 5) Given a subject, predicate, and object, revoke an assertion.
> 6) Create new wrapper objects for resources, literals, and so on.
> 7) Fetch values, types, and so on out of literals.
>
> We should also probably build some convenience tools on top of the
> core
> operations above, and make them available too:
> a) Bags, sequences, etc..., and also containers: append, get at index,
> get next, insert and delete with/without renumbering, etc...
> b) Reification utilities (although we don't use this much for any
> CellML
> specifications, so this is dubious).
> c) Convenience support for cmeta (including Dublin core and vcard),
> simulation metadata, graph metadata.
>
> Any opinions on this would be welcomed.
>
> As a side note for those following the progress of PCEnv:
> PCEnv currently puts serialised RDF/XML into the Mozilla framework,
> and
> then uses Mozilla's frameworks to process this and extract information
> from it. This will work, but only if all the required information is
> nested under the RDF:Description for the model. Unfortunately, this
> means that PCEnv won't be able to change any metadata, because the
> serialiser in Mozilla produces output which isn't compatible with
> this.
> It also means that metadata from models in the repository won't be
> accessible, since 4Suite doesn't nest resources in serialised RDF, but
> instead puts shallow XML for the triples directly into the RDF:RDF
> tag.
> Of course, we could kludge this by getting the document from an RDF
> representation, and then searching for all Description elements in the
> whole model, but it seems wrong that we have to do this.
>
> Best regards,
> Andrew Miller
>
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> cellml-discussion at cellml.org
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