[DAS] Re: Our identifier doc and proposal

Lincoln Stein lstein@cshl.org
Thu, 6 Dec 2001 15:45:47 -0500

Hi Chris,

If you have four different similar but not identical ontologies expressed in 
DAML+OIL, how does a third party provide the equivalence relationships?  Do 
you envision him providing an equivalence apping for each of the 6 pairs, or 
mapping them all to a single common ontology?


On Friday 30 November 2001 18:12, Chris Mungall wrote:
> On Thu, 29 Nov 2001, Ewan Birney wrote:
> > On Wed, 28 Nov 2001, Lincoln Stein wrote:
> > > I think we're going to find that the features form a DAG and not a
> > > hierarchy.  Otherwise you're going to have problems classifying things
> > > like "genes".  In the context of genetics, a gene is a type of
> > > complementation group.  In the context of genomics, a gene is a
> > > subclass of transcription features, translation features, and
> > > regulatory features.
> >
> > Bugger.
> >
> > You are right. I'm glad you are going to sort out how to have an
> > extensible distributed DAG system that is easy to use. ;)
> Thankfully it's already been done - cf semantic web, RDF(S), DAML+OIL etc
> The nice thing about this is if someone doesn't like "ontology
> politburo"'s classes, they can add in their own.
> Two people can develop their own similar class hierarchies without
> speaking to one another, and a third person can provide equivalence
> relationships mapping between the concepts; or logical rules for inferring
> one from the other.
> the DAGs can be as complex as you like, giving computable semantics for
> terms like "tRNA" or just a flat vocabulary, whatever you like.
> Complements DAS beautifully.
> All designed to be anarchic and distributed and not an OMG committee in
> sight
> > DAS mailing list
> > DAS@biodas.org
> > http://biodas.org/mailman/listinfo/das

Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY