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

[Elia Stupka]

> 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).

>   (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?

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)

Elia



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