[Open-bio-l] biosql schema in Oracle

[Ewan Birney]

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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