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

[Matthew Pocock]

Lincoln Stein wrote:
> Chiming in here:
> 
> 
>>>>We do need to discuss assemblies. I vote for "flat" one level
>>>>assemblies
>>>
> 
> I agree.


I would strongly prefer arbitrary depth assemblies. It is the general 
case solution, and biosql is not to my mind the apropreate place to 
special-case data-models (do that in Ensembl or some other 
task-dedicated schema). The BioJava object model supports arbitrary 
depth assemblies, so if we are to use BioSQL to persist BioJava 
seqeuences, BioSQL must support them.

We seem to be comming back to the same modularity issue - if one camp is 
decided upon single-depth assemblies and another camp beleives that 
arbitrary depth assemblies is a requirement then could we not just put 
assembly logic into a seperate chunk of SQL and adapters? We all still 
get to re-use the core tables as-is.

If we had a multi-level-capable schema, how hard is it to execute a 
query at start-up that checks if a depth > 1 is present anywhere? You 
can probably special case this as a self-join on the assembly table, 
group and count - then load in single-level optimized adapters if the 
count is zero.

Matthew