Re: scientific publishing task force update

Hi Eric et al,

The more I think of, would your OntologyCovering task relate to Don 
Doherty's Bridging Ontology task 
(http://esw.w3.org/topic/HCLS/OntologyTaskForce/Create_Bridging_Ontology_between_NeuronDB_and_CoCoDat_databases_and_UMLS_Common_Vocabulary#preview)?

In other words, can your Ontology Covering technique potentially be 
applied to mapping between NeuronDB and CoCoDat OWL ontologies?

Just my 2-cent observation.

Cheers,

-Kei

Eric Neumann wrote:

>
> Following up to Phil's point, an alternative to building upper 
> ontologies (UO) first, is to consider constructing a "Covering Map" 
> between apparent overlapping sets of "related" ontologies. These are 
> light weight, RDF associations that can help "pin-down" potentially 
> related items/classes from different ontologies. I also agree the 
> notion of "guides" is very powerful when dealing with a diverse 
> community, yet trying to get things up and running sooner than later...
>
> I've written this up on the HCLS/OntologyTaskForce wiki:
> http://esw.w3.org/topic/HCLS/OntologyTaskForce/OntologyCovering
>
> As BioRDF progresses in making more life sciences data available as 
> RDF, we will have to deal with such ontological issues more 
> frequently, so it's very useful for everyone to be discussing these 
> issues at this point.
>
> cheers,
> Eric
>
>
>
>
>
> --- Phillip Lord <phillip.lord@newcastle.ac.uk> wrote:
>
> >>>>> "SC" == Steve Chervitz <Steve_Chervitz@affymetrix.com> writes:
>
> >> They also wrote an interesting paper on the state of
> >> bio-ontologies.
> >>
> >> Nature Biotechnology 23, 1095 - 1098 (2005)
> >> doi:10.1038/nbt0905-1095 Are the current ontologies in biology
> >> good ontologies?
> >>
> >> Larisa N Soldatova & Ross D King
>
> SC> Also worth seeing: The MGED ontologies folks wrote a response to
> SC> this article that comments on the bio-ontology development
> SC> process, and addresses some statements Soldatova and King make
> SC> about MO which the MO folks feel are inaccurate or misleading:
>
> SC> Stoeckert C et al. Nature Biotechnology 24, 21 - 22 (2006)
> SC> doi:10.1038/nbt0106-21b Wrestling with SUMO and bio-ontologies
> SC> http://www.nature.com/nbt/journal/v24/n1/full/nbt0106-21b.html
>
> Their paper did cause, how shall I say, somewhat of a stir.
>
>
> SC> The reliance on and choice of upper level ontology seems to be a
> SC> big bone of contention. Are there any good reviews on these
> SC> discussing things like why there are so many of them and why
> SC> can't they be combined? Seems like the current trend is to
> SC> accept their existence and work towards making them
> SC> interoperable:
>
>
> If I were being cynical (those of you who know me will know how rare
> this is), I would suggest that it's a case of "standards are so good,
> that we need one each".
>
> The issue is a slightly deeper one in bio-ontologies. It's not clear
> that an upper ontology actually brings significant value to the
> table. The claimed advantage of interoperability between ontologies
> is, to my mind, somewhat bogus; they only really allow
> interoperability when you are querying over the concepts in the upper
> ontology. Much more important is that they help to ease the design of
> an ontology; you have more idea where concepts should go, so you can
> spend more time worrying about the details of what ever you are
> modelling and less about the big picture.
>
> On the flip side, they tend to complicate some stages of ontology
> development, mostly notably the first month when you have lots of
> biologists tearing their hair out trying to work out what a perjurant,
> continuant, sortal, self-standing kind is.
>
> The juries still out in my opinion.
>
> Phil
>
> Eric Neumann, PhD
> co-chair, W3C Healthcare and Life Sciences,
> and Senior Director Product Strategy
> Teranode Corporation
> 83 South King Street, Suite 800
> Seattle, WA 98104
> +1 (781)856-9132
> www.teranode.com
>

Received on Thursday, 15 June 2006 17:03:51 UTC