[GMOD-devel] Re: [Open-bio-l] Schema for genes & features & mappings to assemblies

[Chris Mungall]

On Tue, 23 Apr 2002, Matthew Pocock wrote:

> Thomas Down wrote:
> > On Mon, Apr 22, 2002 at 02:36:18PM -0700, Hilmar Lapp wrote:
> >
> >>	- biosql is for sequences and features, not mappings to
> >> assemblies (is that intended to be added, too, or is it beyond its scope? )
> >
> >
> > Hi...
> >
>
> > But does mean
> > that all the `assembly-munging' code will probably need
> > to be put in your object layer, rather than handling
> > the assembly directly in the SQL queries.
> >
>
> If Oracle is your target database then you may well be able to use the
> oracle tree-fetching queries to pull out entire assembly trees in one
> hit rather than performing multiple requests. Failing this, a little bit
> of server-side script can be convinced to walk the tree for you (if your
> db admin allows this kind of thing).

Even if you do have n-level assemblies (which most people won't), n will
be fairly low (I've seen arguments for 3 so far, but not 4). You could
just use n-1 view statements rather than relying on non-SQL3 compliant
oracle recursion (I think DB2 is the only database do implement recursive
SQL in an SQL3 compliant way - and no one uses DB2 in bioinformatics as
far as i know)