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

Hi Ben and Matt,

> An RDF version of the  
> UMLS knowledge sources would be seem to be very useful - at 
> least for  
> bioinformatics research purposes ...  

What I was trying to discover was, from a purely RDF/ontology
standpoint, what is gained without any other knowledge of UMLS?  

This question comes more from my ignorance, probably, but when knowledge
gets buried in specialized tags the tendency is that without going to
the source to understand the specialization, what's left is not all that
useful.

cheers,
Michael  

> -----Original Message-----
> From: Benjamin Good [mailto:goodb@interchange.ubc.ca] 
> Sent: Monday, June 05, 2006 12:52 PM
> To: Miller, Michael D (Rosetta)
> Cc: matt@biomedcentral.com; olivier@nlm.nih.gov; 
> public-semweb-lifesci@w3.org
> Subject: Re: BioRDF [Telcon]: slides for the UMLS presentation
> 
> 
> Hi,
> 
> I would tend to agree with Matt on this one.  An RDF version of the  
> UMLS knowledge sources would be seem to be very useful - at 
> least for  
> bioinformatics research purposes - without the benefits of the  
> "correct" OWL ontology with which to describe the relationships  
> included.
> 
> Though there is no doubt that some ontologies are better than others  
> and that there is clear value in investing in building good ones  
> (e.g. a good OWL representation of the UMLS S.N.), the idea that, as  
> a community,  we will ever reach a consensus for the one 
> right way to  
> interpret the relationships in a resource as broad as the UMLS seems  
> unlikely.  It seems to me that if we really want to see the Semantic  
> Web take off in biology, then the first thing is to get as much RDF  
> data accessible online as we can.  Waiting for the perfect 
> ontologies  
> to emerge seems like a non-starter - we have to be able to handle  
> change as well as multiple perspectives in ontologies, so we 
> might as  
> well get started with something.
> 
> 2 cents
> -Ben
> 
> 
> 
> On Jun 5, 2006, at 10:21 AM, Miller, Michael D (Rosetta) wrote:
> 
> > 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
> >>>
> >>>
> >> This email has been scanned by Postini.
> >> For more information please visit http://www.postini.com
> >>
> >>
> >>
> >>
> >>
> >
> 
> 
>

Received on Monday, 5 June 2006 20:05:17 UTC