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

[Elia Stupka]

> Ensembl's sweet spot is assemblies+automatic pipeline (ala Ensembl). Most
> people get put off by how much "stuff" there is inside Ensembl but infact

I just had to jump in here. We over here would be keen and are working on
getting more into bioperl, biosql and bioperl-pipeline. Ideally I think we
should aim at allowing people the same sweet automatic feeling that
ensembl has for genome annotation become one of the many sweet features of
a bioperl-pipeline. With the notable difference that it would be just one
of the many sweet spots in that it could be used also for much smaller
jobs (a simple blast pipeline for lab sequences for example) with the same
ease, and knows how to interact with multiple dbs,etc.

> The big benefits are (a) schema and data which can be downloaded for
> human, mouse, zebra, fugu, (and soon... anopheles) which is guarenteed to
> work (b) very functional web site which is portable (c) ability to run
> automatic systems which scale into a "please completely annotate this
> genome in 2 weeks" scale

I admit I cannot see any of us or bioperl moving soon to some fancy
website building and it'd be useless. Probably more on the lines of
genquire, or a bioperl-gui... but apart from that there would be no issue
once things are setup to port bioperl-pipeline over to ensembl with a
couple of parsers or the other way around.

Elia



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