[DAS] Re: Our identifier doc and proposal

[Chris Mungall]

On Thu, 6 Dec 2001, Lincoln Stein wrote:

> 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?

The all by all approach would rapidly get out of hand. I think your idea
of mapping to a skeleton ontology is best. One can imagine all kinds of
different toplogies but that would be getting ahead of ourselves. The
important point is that the level of conformance should be optional.
 
> Lincoln
> 
> 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
> 
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