Re: scientific publishing task force update

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