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RE: [BioRDF] UML/RDF [Was: Meeting Notes Feb 27, 2006]

From: Miller, Michael D (Rosetta) <Michael_Miller@Rosettabio.com>
Date: Thu, 2 Mar 2006 10:37:22 -0800
To: "Cutler, Roger (RogerCutler)" <RogerCutler@chevron.com>, wangxiao@musc.edu, "public-semweb-lifesci" <public-semweb-lifesci@w3.org>
Message-ID: <E1FEsg8-0006Kv-UL@aji.w3.org>

Hi All,

For me, my interest was in the transformation of an RDF XML document to
the equivalent (to some measure of equivalent) UML XML document and back
to describe/define an ontology.

The practical problem with the RDF XML notation we ran into for our use
is that many of the XML element names are dependent on the class and/or
property names in the ontology, so every ontology would need to have its
own XML Schema to validate the document. 

Our use case for MAGE-ML (generated from the MAGE-OM UML model) is to
simply allow creating and/or referencing individuals based on arbitrary
ontology classes (http://mged.sourceforge.net/).  Not arbitrary to the
user but arbitrary as far as applications based on MAGE.  So we needed a
formulation in our model that was not dependent on RDF specific XML

Since we have no interest in incorporating entire ontologies, only
referencing, our needs are a bit simpler than probably a lot of other
folks.  In fact, it was only the Individual diagram from an earlier
draft, which has been deprecated but still described in "17.2.4
InstanceSpecification", that is the basis for what will be used in the
FuGE-OM UML model follow-up to MAGE-OM (http://fuge.sourceforge.net/).

The specification is also useful for thinking how arbitrary ontologies
can be referenced from relational or object databases without needing
foreknowledge of particular ontologies.


Michael Miller
Lead Software Developer
Rosetta Biosoftware Business Unit

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org 
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> Cutler, Roger (RogerCutler)
> Sent: Thursday, March 02, 2006 7:34 AM
> To: wangxiao@musc.edu; public-semweb-lifesci
> Subject: [BioRDF] UML/RDF [Was: Meeting Notes Feb 27, 2006]
> This lengthy and dense, but generally very well written, document goes
> into extreme detail as to the similarities and differences between UML
> and "RDF" (which I take to be a blanket term encompassing 
> other Semantic
> Web specs).  I'm not by any means an expert, but it looked to me like
> there are very significant overlaps in both detail and general
> philosophy of approach and implementation.  I got the impression, but
> this is by no means spelled out, that this document is an artifact of
> the process of the UML folk getting "on board" the SW train.  It
> certainly represents a very impressive amount of effort in 
> preparation. 
> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> Xiaoshu Wang
> Sent: Wednesday, March 01, 2006 1:24 PM
> To: 'public-semweb-lifesci'
> Subject: RE: [BioRDF] Meeting Notes Feb 27, 2006
> - Michael,
> > http://www.omg.org/docs/ad/05-09-08.pdf
> > 
> > Because it is still being evaluated, this might only be 
> available from
> > the OMG website to OMG members.
> Thanks.  I was able to get the document.  Though haven't read through
> yet, it is too long ( closed to 300 pages ) but I spotted one heading
> from the
> document:
> 8.2 Why Not Simply Use or Extend the UML 2.0 Metamodel?
> To me, it implies that 
> RDF != UML 4.0? 
> Xiaoshu
Received on Thursday, 2 March 2006 18:37:38 UTC

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