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[HCLS] RE: scientific publishing task force update

From: Donald Doherty <donald.doherty@brainstage.com>
Date: Sat, 29 Jul 2006 20:37:25 -0400
To: "'w3c semweb hcls'" <public-semweb-lifesci@w3.org>
Message-ID: <000d01c6b370$546a9ce0$6401a8c0@Brainstage>

Kei is correct that there is overlap in the approach I think we're taking to
and Eric's ideas. My mentor Karl Pribram wrote about neuroscience as a
modern day "Tower of Babel" in his 1972 "Languages of the Brain."

Not only is the situation is much the same today but I don't believe that
will ever change (nor would it be desirable if it did...we need all of the
ideas, viewpoints, etc. that we can get). So, there will always be multiple
ontologies that change over time (some slowly some not).

That is why it seems especially important to provide a way to build bridges
between ontologies that enable individuals and organizations to contemplate
more than one semantic view of any given dataset.

[Please ignore the above if this has been covered already...I'm currently
trying to catch up with about one and a half months of email! I had to
finish a prototype that is now in debug hell...but that's another story.]


Donald Doherty, Ph.D.
Brainstage Research, Inc.

-----Original Message-----
From: public-semweb-lifesci-request@w3.org
[mailto:public-semweb-lifesci-request@w3.org] On Behalf Of kei cheung
Sent: Thursday, June 15, 2006 1:04 PM
To: Eric Neumann
Cc: Phillip Lord; w3c semweb hcls
Subject: 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 

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

Just my 2-cent observation.



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 Sunday, 30 July 2006 00:35:37 UTC

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