[Biojava-l] SQL-backed persistent Biojava sequence/feature objects

[Ewan Birney]

On Mon, 30 Jul 2001, David Huen wrote:

> On Mon, 30 Jul 2001, Thomas Down wrote:
> 
> > On Mon, Jul 30, 2001 at 01:48:57PM +0100, Ewan Birney wrote:
> > >
> > 
> > David, have you looked at the BPDB schema?  How welll do you
> > think it meets your needs?
> > 
> I haven't looked at the BPDB schema yet, I'll try to do that this evening.
> To save me navigating thru a framework for a package in a language I don't
> understand, do you have a URL to the relevant SQL schema please?

check out bioperl-db from anonymous cvs and then the sql/basic-mysqldb.sql

I'll send it to you.

> 
> Will Ewan and you be down at the Brocklehurst beer bash on Wed?  Perhaps
> it might be easier to trash out with a pad of paper how far we can achieve
> commonality without extreme complexity.
> 

Apologies no. I am in california :(


> What design I've got so far is a pretty direct mapping of Biojava
> sequence/feature objects onto a database and relies on using sequence and
> feature ids to get a hierarchy (features have parent fields so select on
> that field gets me the next level) and as you mentioned, a BLOB to chuck
> the bundle into (I was tempted to use a BLOB for an entire sequence but
> that's taking the piss and not very editable).  I'm trying to make it such
> that I can either choose some form of lazy instantiation for Biojava
> objects (and save memory at the expense of more database transactions) or
> have the whole sequence object instantiated at a go.  I'm trying to keep
> it simple as I'm sure I'll find design errors necessitating a rewrite and
> I'd rather that happened earlier rather than later when a lot has been
> invested into a design.  The primary objective for me is that other than
> the original call to get such an object, all subsequent manipulations
> should as if you were working on a standard Biojava object.

Take a look at bioperl-db. It aint so bad ;)