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Quoting Matt Halstead
<matt.halstead AT auckland.ac.nz>:

> Yes, we leave it as XML fragments for now
So you are suggesting that I use something like:

typedef dom::Element RDF;

to define RDF?

> and deal with it when we
> come to thinking about handling metadata. We are likely to want to
> add a CellML specific API for metadata based on either RDF schemas,
> or OWL ontologies.
I'm not sure that we want to restrict the API to what is defined in the CellML
Metadata specification, but perhaps we could use a general API, include a
mechanism for namespace based delegation of the implementation(as is done with
the DOM, for example, to implement MathML), and provide a CellML specific as
well as a generic API.
> The CellML metadata editor does have an interface
> for handling the metadata, and that might be a good place to review
> some of this when the time comes.
The problem is that unless we define the API well now, API users will rely on
the current behaviour, and then break when future versions of the API come
out.
So I think we do need to at least define an extensible mechanism for dealing
with RDF, even if we don't actually extend it to do CellML metadata specific
handling yet.

Best regards,
Andrew Miller


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>From ak.miller at auckland.ac.nz Fri Aug 26 18:23:17 2005
From: ak.miller at auckland.ac.nz (Andrew Miller)
Date: Fri Aug 26 18:23:20 2005
Subject: [cellml-discussion] CellML API: Should cellmlVersion be read-only.
Message-ID:
<1125037397.430eb555da7f2 AT www.bioeng.auckland.ac.nz>

It seems to me that cellmlVersion should be read-only, for consistancy with
the
way that XML is generally used(for example, in the DOM).

In the DOM, once an element is created, the qualified name(namespace and local
name) are immutable. Hence, if you need to change the namespace of an element,
you need to create a new element, and copy all the the data from that element
into the new element, and then replace the old element with the new element.
This choice is quite deliberate, because elements can be inherited from, and
the type of the element depends upon its qualified name. If you could change
the namespace arbitrarily, you could be changing the type of a node just by
setting a variable(which is incompatible with both the design of many systems,
and is confusing for users).

However, to change the CellML version of an element, we do have to change the
namespace.

It seems, therefore, that we should not allow individual CellMLElements to
arbitrarily be changed from one CellML version to another(and if you are using
the DOM for our implementation, then the node in the DOM model will be
unexpectedly replaced).

Best regards
Andrew Miller


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>From matt.halstead at auckland.ac.nz Fri Aug 26 20:40:29 2005
From: matt.halstead at auckland.ac.nz (Matt Halstead)
Date: Fri Aug 26 20:40:33 2005
Subject: [cellml-discussion] RDF API
In-Reply-To:
<1125036553.430eb2093976a AT www.bioeng.auckland.ac.nz>
References:
<1125030905.430e9bf9047f4 AT www.bioeng.auckland.ac.nz>

<2A730386-5C50-44E2-B318-D8F661442836 AT auckland.ac.nz>

<1125036553.430eb2093976a AT www.bioeng.auckland.ac.nz>
Message-ID:
<76C42A6E-E202-4DB2-86AE-E3B8BF4E5A66 AT auckland.ac.nz>


On 26/08/2005, at 6:09 PM, Andrew Miller wrote:



> Quoting Matt Halstead
> <matt.halstead AT auckland.ac.nz>:
>
>
>
>
>> Yes, we leave it as XML fragments for now
>>
>>
>>
> So you are suggesting that I use something like:
>
> typedef dom::Element RDF;
>
> to define RDF?
>
>

That would do fine.




>
>
>
>
>> and deal with it when we
>> come to thinking about handling metadata. We are likely to want to
>> add a CellML specific API for metadata based on either RDF schemas,
>> or OWL ontologies.
>>
>>
>>
> I'm not sure that we want to restrict the API to what is defined in
> the CellML
> Metadata specification, but perhaps we could use a general API,
> include a
> mechanism for namespace based delegation of the implementation(as
> is done with
> the DOM, for example, to implement MathML), and provide a CellML
> specific as
> well as a generic API.
>
>

I'm not suggesting it is restricted, that's another question
altogether. An RDF schema handler would be sufficient for exposing an
API for creating CellML metadata. But lets not worry about that now.




>
>
>
>> The CellML metadata editor does have an interface
>> for handling the metadata, and that might be a good place to review
>> some of this when the time comes.
>>
>>
>>
> The problem is that unless we define the API well now, API users
> will rely on
> the current behaviour, and then break when future versions of the
> API come out.
> So I think we do need to at least define an extensible mechanism
> for dealing
> with RDF, even if we don't actually extend it to do CellML metadata
> specific
> handling yet.
>
> Best regards,
> Andrew Miller
>
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion AT cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion
>
>
>

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• [cellml-discussion] RDF API, Andrew Miller, 08/26/2005
  • Re: [cellml-discussion] RDF API, Matt Halstead, 08/26/2005
    • [cellml-discussion] RDF API, Andrew Miller, 08/26/2005
      • Re: [cellml-discussion] RDF API, Matt Halstead, 08/26/2005

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