[Open-bio-l] Schema for genes & features & mappings to assemblies

[Ewan Birney]

On Tue, 23 Apr 2002, Elia Stupka wrote:

> > I *do* think people will be surprised and how clean the next generation
> > Ensembl schema is, which we are working on in a very steady manner and
> 
> I do love it too, so much more in line with every other schema we have
> written since the Arne revolution ;)
> 
> > We do need to discuss assemblies. I vote for "flat" one level assemblies
> 
> I guess the other bit missing from biosql at the moment is gene
> structures, to really start thinking of being able to do things only with
> biosql.
> 
> I would diverge about aseemblies, like the hierarchical structure,
> especially if I think of making our pipeline work with biosql, because it
> would allow small projects to run a pipeline that assembles reads into
> contigs, and then on top of that has other assemblies and standard
> annotation pipelines. An example that will hit us very soon is that we
> want to setup a little finishing thing for Fugu, so finishing data would
> come in, we'd phrap it, stitch the scaffolds that need stitching,
> re-annotate, and go on. There it'd be nice, (though of course there is a
> hundred ways to get around it and manage anyway, by splitting it to
> different dbs which might be cleaner anyway).

This is the point - I don't think the heirarchy buys you anything here
except the warm fuzzies that it "feels like a heirarchy" - when in fact it
is not really.

> 
> >   (b) zero level (Lincoln likes this). The schema stores contigs as
> > "features" on DNA Sequences which are chromosome length.
> 
> But with zero level reverse-engineering is hard, if you want to, for
> example, do a local update, right?
> 

yup

> I think zero level is suitable for what comes later, data mining, which is
> what we are planning to do for our multi-genome data-mining
> pipeline. Because by that stage you really cannot care less why the
> coordinates are what they are, you just want to use them (a la
> ensembl-lite)
> 

Bro speaks the truth...


> Elia
> 
> 
> 
> > 
> > 
> > 
> > 
> > > Elia
> > > 
> > > 
> > > 
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> > 
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>. 
> > -----------------------------------------------------------------
> > 
> 
> -- 
> ********************************
> * http://www.fugu-sg.org/~elia *
> * tel:    +65 874 1467         *
> * mobile: +65 90307613         *
> * fax:    +65 777 0402         *
> ********************************
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> 
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
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