Re: [Gmod-schema] Re: unique dbxref_id on cvterm

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

On Tue, 2005-02-22 at 08:13 -0800, Chris Mungall wrote:
> > >
> > > A cv.name should never be "Ad hoc" because there will be collisions
> > > between cvs
> >
> > Fair enough.  Would you prefer 'local'?
> 
> Sorry, I was being cryptic. What I meant was, even these "ad hoc"
> ontologies must have some kind of name that communicates the nature of the
> cvterms within them. It seemed like you were planning on lumping all
> ad-hoc ontologies together, which has a high likelihood of producing
> collisions on cvterm unique keys.
> 
> It sounds like "Ad hoc:synonym" is actually from a cv of property types
> that can be attached using featureprop et al. This is very definitely not
> an ad-hoc ontology, it's crucial that featureprop types have their own cv
> and are defined

Actually, I only have a few things in 'local'.  They are things that are
fundamental to making chado work (or the gff loader work), like score
and synonym.  There are several other ad hoc ontologies that have more
descriptive names like 'property type', and 'Statistical terms'.  I
think this arrangement makes as much sense as FlyBase chado's use of the
synonym type ontology with exactly one term in it: synonym.

Darn it, as soon as I wrote that last sentence, I was reminded of how
it's not true: Lincoln was complaining to me a few months ago about
WormBase's lack of typed synonyms.  He said it would be nice to have
'GenBank synonym', 'Swissprot synonym', etc.  I happily pointed out that
chado could easily do that.

Scott

-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         ca...@cs...
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory