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Re: Cheers and Concerns

From: Dan Connolly <connolly@w3.org>
Date: 02 May 2002 10:04:00 -0500
To: Autumn Cuellar <a.cuellar@auckland.ac.nz>
Cc: public-webont-comments@w3.org
Message-Id: <1020351842.29626.2797.camel@dirk>
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On Wed, 2002-04-17 at 23:34, Autumn Cuellar wrote:
> Hello,
> I was very happy to learn of your group's massive undertaking, as I've
> tried to use RDF Schema and DAML+OIL in defining an XML ontology for an
> XML-based biological modelling language we're developing, and both have
> fallen short in areas.  So you know where I'm coming from: we have
> already done the work (released a specification) for a language that
> describes cellular models.  We're interested in using ontologies to not
> only describe the language that we've created, but to continue to add to
> that language.  For instance, we have the ability to describe reactions,
> now we want to add the ability to import a commonly used reaction. 
> First we have to be able to define what those commonly used reactions
> are.  Anyways, enough about my work and on to yours....
> I wanted to bring up a couple of problems I've had in the past, and
> maybe others have had these problems and they might be worth discussing:
> 1)  I've found the common way of referencing attributes and elements in
> a namespace inconvenient (url#element_name, or
> http://www.example.org/attribute_name).  Perhaps rather short-sightedly,
> we've given elements and attributes the same name, so you can see the
> problem that arises when you're trying to describe two different
> concepts (an element with the name of "units" and an attribute with the
> name of "units") with an rdf:about="http://www.example.org#units". 
> According to the XML namespace spec
> (http://www.w3.org/TR/1999/REC-xml-names-19990114/), these two "units"
> could be given their expanded names which would establish that they are
> not the same, but how do you reference the expanded names in an
> rdf:about attribute?  This is possibly an issue that I should raise
> elsewhere (suggestions on where?) and is probably out of the scope of
> your intentions, but it is an issue that could affect any ontologies
> built with your language.
> 2)  Scientific groups using XML, of which I am sure there are more than
> a few, might find it helpful to be able to define things in an ontology
> mathematically, for instance, one thing is a ratio of two other things. 
> Have you considered allowing the use of MathML in an ontology language?  
> 3)  I'm supportive of your use of DAML+OIL, but the one complaint I have
> about DAML+OIL is their method of using user-defined datatypes
> (referencing an XML Schema file).  They suggest referencing a class that
> hasn't been specifically defined as such.  Additionally, I would prefer
> to define the datatypes in the same file.
> 4)  Will import capabilities (of other ontologies) be dealt with at some
> point?  Can't imagine you'd create a web ontology without import
> capabilities, but I want to make sure it's somewhere on your list.
> Cheers for your efforts so far.  I like what I'm seeing and will coninue
> to watch your progress closely.
> Best wishes,
> Autumn
> -- 
> Autumn A. Cuellar
> Bioengineering Institute
> The University of Auckland
> New Zealand
> www.cellml.org
Dan Connolly, W3C http://www.w3.org/People/Connolly/
Received on Thursday, 2 May 2002 11:03:44 UTC

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