[Bioperl-l] Re: BioSQL or chado

[Ewan Birney]

>
> ensembl is a different kettle of fish altogether. The main difference is
> that typing is enforced at the relational layer in ensembl. this has many
> advantages and disadvantages which have been discussed to death, it
> depends on your project really.
>
> ensembl is the most mature, and chado is the new kid on the block.
> however, chado 1_01 has just been frozen, and that's what most apps will
> be targetting.
>

ensembl is also strictly targetted at "storing features on genome
sequence" whereas BioSQL has a broader "storing biological stuff" target.
Ensembl has been in fact drifting away from Bioperl towards just
supporting an extremely clean Perl and Java API on-top of its
highly-relational focused schema. The bioperl compatibility is now really
around the edges. I may, over the same, build a explicit standalone bridge
between Ensembl and Bioperl which would provide all the usual Bioperl
interfaces from this pretty vanilla schema.


So...

  Storing Just Genomes --- choose between Chado and Ensembl, with
undoubtly Ensembl having the current most mature tool sets (including
loaders now from particular flavours of GenBank/EMBL format)

  Storing "any" sequence --- BioSQL or roll your own.