RE: BioRDF [Telcon]: slides for the UMLS presentation

Hi All,

> But presumably the relations which characterize the structure 
> of UMLS could be given their own URIs, no?
> Along with the concepts themselves.
> 
> And then UMLS could then be expressed in RDF, using UMLS 
> specific relations, rather than standard OWL relations.

This, of course, works to a certain extent but brings up an issue that I
think will significantly impact end users and the adoption of
ontologies.

One can get a rudimentary idea of a annotation source using standard RDF
tools through this sort of representation but that will miss the actual
semantic value that is embedded in domain specific relations.

> It would then at least be URI-ified and so connected into the 
> RDF-universe, and different implementors could experiment 
> with different approximative mappings to OWL relationships, 
> for some or all of UMLS, according to their particular needs.

The end user is now back to having to go to the source itself, so why
bother setting up this approximate mapping?

I've noticed a creep from several RDF representations to using these
domain specific relations which means needing a one-off parsing of each
one to get the true semantics.

This seems to defeat the purpose.

cheers,
Michael

Michael Miller
Lead Software Developer
Rosetta Biosoftware Business Unit
www.rosettabio.com

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org 
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> matt@biomedcentral.com
> Sent: Monday, June 05, 2006 10:06 AM
> To: olivier@nlm.nih.gov; goodb@interchange.ubc.ca
> Cc: public-semweb-lifesci@w3.org
> Subject: RE: BioRDF [Telcon]: slides for the UMLS presentation
> 
> 
> 
> But presumably the relations which characterize the structure 
> of UMLS could be given their own URIs, no?
> Along with the concepts themselves.
> 
> And then UMLS could then be expressed in RDF, using UMLS 
> specific relations, rather than standard OWL relations.
> 
> It would then at least be URI-ified and so connected into the 
> RDF-universe, and different implementors could experiment 
> with different approximative mappings to OWL relationships, 
> for some or all of UMLS, according to their particular needs.
> 
> There might, for example, be some well defined bits of UMLS 
> where the relations can be reasonably mapped to is_a and 
> part_of relations.
> 
> Matt
> 
> > -----Original Message-----
> > From: public-semweb-lifesci-request@w3.org
> > [mailto:public-semweb-lifesci-request@w3.org]On Behalf Of Olivier
> > Bodenreider
> > Sent: 05 June 2006 18:00
> > To: Benjamin Good
> > Cc: 'public-semweb-lifesci'
> > Subject: Re: BioRDF [Telcon]: slides for the UMLS presentation
> > 
> > 
> > 
> > Benjamin Good wrote:
> > > Are there any plans to release the UMLS or parts thereof as 
> > RDF / OWL ?
> > Not to my knowledge, Ben. And I certainly would be very 
> > cautious of any 
> > attempt to doing it. The main reason is that many relations 
> used for 
> > creating hierarchies in biomedical vocabularies are not true 
> > hierarchical relations (isa, part_of), but simply reflect 
> the purpose 
> > for which these terminologies were created. For example, it 
> > makes sense 
> > in MeSH (i.e., for information retrieval) to have "accident 
> > prevention" 
> > listed as a child of "accidents". It would be wrong to assume 
> > that all 
> > child_of relations can be represented by subclassof 
> relations. And an 
> > accurate representation of MeSH in OWL would be difficult to obtain.
> > 
> > -- Olivier
> > 
> > 
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Received on Monday, 5 June 2006 17:21:34 UTC