[DAS] Re: Our identifier doc and proposal

[Lincoln Stein]

OK, so that argues that we need to develop a common ontology to work from, 
right?  I was beginning to think that the sentiment was that DAS should *not* 
develop an ontology of annotation types.

Lincoln

On Thursday 06 December 2001 17:07, Chris Mungall wrote:
> 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
> >
> > NOW HIRING BIOINFORMATICS POSTDOCTORAL FELLOWS AND PROGRAMMERS.
> > PLEASE WRITE FOR DETAILS.
> > ========================================================================

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

NOW HIRING BIOINFORMATICS POSTDOCTORAL FELLOWS AND PROGRAMMERS. 
PLEASE WRITE FOR DETAILS.
========================================================================