- From: Robert Stevens <robert.stevens@manchester.ac.uk>
- Date: Tue, 13 Jun 2006 13:15:41 +0100
- To: Steve Chervitz <Steve_Chervitz@affymetrix.com>, Phillip Lord <phillip.lord@newcastle.ac.uk>, Mark Musen <musen@stanford.edu>
- Cc: AJ Chen <canovaj@gmail.com>,<public-semweb-lifesci@w3.org>
The range of upper ontology reflects the different philosophical viewpoints on the nature of what exists in the world. Different upper ontologies make different distinctions. Most of the upper ontologies have a great deal in common, but different philosophies make different distinction and even given the same distinctions different labels. One small, but significant, dislike of the bio-ontology community for SUMO (as used by Solditova and King) is that it isn't really only an upper level. It strays into, for instance, stating a protein is a foodstuff. this, as you might suppose, causes biologists to laugh. Robert. At 21:23 12/06/2006, Steve Chervitz wrote: >Phillip Lord <phillip.lord@newcastle.ac.uk> on Mon, 12 Jun 2006: > > > >>>>>> "MM" == Mark Musen <musen@stanford.edu> writes: > > > > MM> A colleague just pointed me to this (rather vacuous) article. > > MM> Does anyone know more about this work? > > MM> http://www.newscientisttech.com/article/dn9288-translator-lets- > > MM> computers-understand-experiments-.html > > > > It's a middle ontology for describing experiments--hypothesis, > > conclusions that sort of thing. Larisa Soldatova and Ross King have > > been working on this for a couple of years. As some one else > > mentioned, it fits in with Ross' earlier work on a robot scientist > > which was really very nice. > > > > 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 > >Also worth seeing: The MGED ontologies folks wrote a response to this >article that comments on the bio-ontology development process, and addresses >some statements Soldatova and King make about MO which the MO folks feel are >inaccurate or misleading: > >Stoeckert C et al. Nature Biotechnology 24, 21 - 22 (2006) >doi:10.1038/nbt0106-21b >Wrestling with SUMO and bio-ontologies >http://www.nature.com/nbt/journal/v24/n1/full/nbt0106-21b.html > >The reliance on and choice of upper level ontology seems to be a big bone of >contention. Are there any good reviews on these discussing things like why >there are so many of them and why can't they be combined? Seems like the >current trend is to accept their existence and work towards making them >interoperable: > >http://ontolog.cim3.net/cgi-bin/wiki.pl?UpperOntologySummit > >Steve
Received on Tuesday, 13 June 2006 12:16:53 UTC