[Gmod-schema] Re: [Bioperl-l] Re: BioSQL or chado

[David Emmert]

I'm coming in on the cross-post, so please forgive me if I'm repeating
something thats already been said...


On 07/30/03 at 12:47 AM Ewan Birney wrote:
>
>  >
>  > 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.
>

Exactly right.  And what distinguishes chado from ensembl is that chado
is being designed to integrate genetic/phenotypic literature curation
data with genome data.

With respect to genome sequence and annotation data in chado, bioperl
bindings are only now emerging.  The genetic module of chado is itself
still evolving, and as far as bioperl goes, being extremely sequence/
annotation-centric, there are no classes to handle this sort of data.
Once we've got the chado genetic module implemented, it'll be very
interesting to see how bioperl might be extended to handle integrated
genomic/genetic data.

-Dave

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