[BioSQL-l] UK definition for seqfeature

[Aaron J Mackey]

Right, sorry, I forgot we're talking about FK's into term table, not
source/type strings.

I'm liking the idea of a "biosql"-namespaced set of terms, prepopulated in
the schema, including a generic "unknown" or "undefined".

But for now just make the darn FK NOT NULL so that our precious UNIQUE
constraints will work.

-Aaron

On Tue, 18 Mar 2003, Hilmar Lapp wrote:

> type_term_id is supposed to reference an SO term. source is supposed to
> denote the 'method'  (BLAST, BLAT, sim4, genewise, whatnot), as far as
> my understanding goes. In the case of reading the features from a
> GenBank feature table, assigning 'Genbank/EMBL/Swissprot' as the source
> (which is what the genbank, embl, and swissprot parsers do in bioperl)
> is maybe stretching the definition, but I don't have something
> substantially better to offer.
>
> BTW there is no sensible default here. A term cannot have an empty name
> (once you step outside the neat MySQL world). If you want to press hard
> for a default, you could use 'unknown' or 'anonymous' (in an ontology
> of feature sources - hmm...)
>
> 	-hilmar
>
> On Tuesday, March 18, 2003, at 04:42  AM, Aaron J Mackey wrote:
>
> >
> > Of course some will argue that type_term and source_term should really
> > just be qualifier values, in a data-format agnostic viewpoint (and I've
> > never really understood the whole type/source dichotomy; my GFF files
> > are almost always wrong).
> >
> > But I have no objection to making it NOT NULL DEFAULT "" (term as
> > well).
> >
> > -Aaron
> >
> > On Mon, 17 Mar 2003, Hilmar Lapp wrote:
> >
> >> There is currently a compound unique key defined on seqfeature
> >> comprising of (bioentry_id,type_term_id,source_term_id,rank).
> >>
> >> A while ago all but the first were nullable columns with the
> >> previously
> >> known problems of different behaviour between RDBMSs. The situation is
> >> much clearer defined now, as only source_term_id is left as nullable.
> >>
> >> Can anyone name reasons why we should leave this column nullable?
> >> I.e.,
> >> can people think of sensible use cases where you would not have a
> >> source_tag for a feature?
> >>
> >> I believe even in GFF source is mandatory ...
> >>
> >> 	-hilmar
> >>
> >>
> >
> > --
> >  Aaron J Mackey
> >  Pearson Laboratory
> >  University of Virginia
> >  (434) 924-2821
> >  amackey at virginia.edu
> >
> >
> >
>

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