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

[Thomas Down]

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...

There was a bit of discussion of assemblies at Cape Town,
but I don't think it was terribly conclusive.

I did actually write a little BioSQL schema extension
for supporting assemblies, and prototyped some support for
it in the BioJava-BioSQL code.  So it's certainly possible.
The particular approach I took wasn't universally well
received, though, since I designed it to support nested
assemblies (i.e. a fragment of an assembly can itself be
an assembly).  That's nice in that you can actually model
the whole assembly process (right down to the individual
sequencing reads, if you feel like it). 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 you think BioSQL + assemblies might fit your requirements,
it could be worth re-starting this debate.

    Thomas.