[BioSQL-l] more consistency

[Aaron J Mackey]

> Both are OK with me. These are all legacy names.

Great; then the proposal is to a) search and replace ontology_term with
term (which also brings term_id into sync with seqfeature's source_term_id
and type_term_id) and b) change ontology_dbxref to term_dbxref

> Note, however, that a term should live in an ontology for the sake of a
> consistent unique key. If it's not a NOT NULL column already, I suggest
> to make the foreign key from Ontology_Term to Ontology mandatory.

Ahh yes, I see: the ontology_term table name turning into simply "term";
hmm, not so sure about that.  I was thinking more of all the
"ontology_term_id" foreign keys sprinkled about.  But to be a true bugbear
about consistency, I think I'd have to alter my proposal to the much more
verbose: a) change ontology_dbxref to ontology_term_dbxref and b) change
seqfeature's source_term_id to source_ontology_term_id (and
type_ontology_term_id)

But the ontology/term nomenclature isn't so bad if you consider it a
mirror of biodatabase/bioentry (i.e. it's not
biodatabase/biodatabase_bioentry).  So there you have it, two opposing
arguments for two distinct proposals.  Discuss.

-Aaron

>
> 	-hilmar
>
> On Tuesday, March 11, 2003, at 12:49  PM, Aaron J Mackey wrote:
>
> >
> > I notice that a dbxref for an ontology term is in ontology_dbxref, not
> > ontology_term_dbxref (I'd think that ontology_dbxref was a dbxref for
> > the
> > ontology, not terms in the ontology).
> >
> > Proposal: ontology_dbxref renamed to ontology_term_dbxref
> >
> > Alternative proposal: ontology_term be replaced with term (which is a
> > more
> > generic concept, that may or may not be involved in an ontology).
> >
> > -Aaron
> >
> > --
> >  Aaron J Mackey
> >  Pearson Laboratory
> >  University of Virginia
> >  (434) 924-2821
> >  amackey at virginia.edu
> >
> >
> > _______________________________________________
> > BioSQL-l mailing list
> > BioSQL-l at open-bio.org
> > http://open-bio.org/mailman/listinfo/biosql-l
> >
>

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey at virginia.edu