[Open-bio-l] biosql schema in Oracle

[Lincoln Stein]

Can we strive for full roundtripping of the ASN.1 model, or is it subject to 
the same semantic ambiguities as the flatfile representation?

Lincoln

On Monday 12 August 2002 09:32 am, Ewan Birney wrote:
> On Mon, 12 Aug 2002, Matthew Pocock wrote:
> > Hi.
> >
> > I am interested in and have used BioSQL for orthogonal persistance of
> > BioJava sequence object & feature hierachies. Also, I've used it to
> > store swissprot. I am only interested in storing genbank & swissprot via
> > the existing biojava sequence object APIs, and for my needs don't have
> > full ascii-art round tripping of these file formats as a requirement.
> > Semantic round tripping would be good, but this (imho) is best done by
> > having semantic round tripping from the file format to the object layer
> > and between the object layer and biosql. Note, I do not have sematic
> > identity as a requirement, just round tripping. Are we going to put a
> > use cases document (intended, actual and wish-list) together?
>
> This is definitely a good start. I would like to add:
>
>
>  "As good as possible ascii roundtripping, with documented reasons where
> and why we don't ascii round trip"
>
>
> So - a weaker requirement than full round tripping, but still basically
> catching the essentially idea of "storing genbank in a database"
>
> > Matthew
> >
> > Hilmar Lapp wrote:
> > > So, you're calling for a use-case document listing what gave rise to
> > > the design?
> > >
> > > Has something like that been written up by anyone of the original
> > > hackathon participants?
> > >
> > >     -hilmar
> > >
> > > On Saturday, August 10, 2002, at 07:39  AM, Wiepert, Mathieu wrote:
> > >> I want to suggest that you make it clear that the bioSQL schema was
> > >> originally designed to support genbank data, and not anything more.
> > >>
> > >>
> > >> -Mat
> >
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> -----------------------------------------------------------------
> Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> <birney@ebi.ac.uk>.
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