[Gmod-schema] Re: unique dbxref_id on cvterm

[Scott C. <ca...@cs...>]

On Mon, 2005-02-21 at 19:49 -0800, Chris Mungall wrote:
> 
> On Mon, 21 Feb 2005, Scott Cain wrote:
> 
> > On Mon, 2005-02-21 at 19:18 -0800, Chris Mungall wrote:
> > > the dbxref must be persistent and consistent across database
> > > instances
> >
> > Why?  By there very nature, they are going to be the sort of thing that
> > are locally used and not global.  If they were more generally used, they
> > should be on OBO.
> 
> Not necessarily. If you look at most of the non-obo ontologies out there
> typically available in OWL format, most conflate the name and ID
> 
> > > what about making dbxref = cv.name + cvterm.name?
> >
> > Seems ugly.  So an accession of "Ad Hoc Ontology:synonym" is what you
> > are suggesting?
> 
> Eh?
> 
> A cv.name should never be "Ad hoc" because there will be collisions
> between cvs

Fair enough.  Would you prefer 'local'?
> 
> > >
> > > On Mon, 21 Feb 2005, Scott Cain wrote:
> > >
> > > > Hi Chris,
> > > >
> > > > I am dreading writing this email a little bit, given the discussion that
> > > > occurred a few weeks ago involving dbxrefs and cvterms.  Anyway, I
> > > > gather from the comments you added to cvterm that you really did intend
> > > > to make a unique index on dbxref_id in cvterm, and I even understand why
> > > > you did it given that much of the time, the cvs are coming from a real
> > > > ontology and they have accessions.  Of course, some of the time, there
> > > > will be "ad hoc" cvs that won't have accessions.  The solution I am
> > > > suggesting is the creation of a db sequence and items that don't belong
> > > > to a formal ontology will get the next available value from the
> > > > sequence.  Does that sound OK to you?
> > > >
> > > > Thanks,
> > > > Scott
> > > >
> > > >
> > >
> >
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory