- From: Olivier Bodenreider <olivier@nlm.nih.gov>
- Date: Mon, 05 Jun 2006 17:37:23 -0400
- To: Benjamin Good <goodb@interchange.ubc.ca>
- CC: "Miller, Michael D (Rosetta)" <Michael_Miller@Rosettabio.com>, matt@biomedcentral.com, public-semweb-lifesci@w3.org, "Rindflesch, Tom" <tcr@nlm.nih.gov>
As much as I was opposed to OWLizing the UMLS, I agree that it would be doable and certainly useful to RDFize it. My group at NLM is actually working on something similar as part of a larger project where we develop a repository of facts extracted from the literature, terminologies and structured databases. -- Olivier Benjamin Good wrote: > 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 21:37:34 UTC