[Bioperl-l] UCSC database -> GFF

Ewan Birney birney at ebi.ac.uk
Thu Jun 19 10:04:43 EDT 2003

On Wed, 18 Jun 2003, Lincoln Stein wrote:

> Hi Allen,
> I hope someone (Mummi?) will pick it up.  It's necessary now that NCBI has
> decided to make their human annotations effectively unloadable.  Maybe
> ENSEMBL can have a look at their EMBL output and try to find a way to get
> more track info into it?

No way. We have a very, very good and sane Perl API which people could
wrap for more Bioperl-ness, and we have a very, very sane schema and a
denormalised schema for sensible things. We are not going to keep
extending EMBL format and bounce things through that. Asking for trouble.

Ensembl has a very sensible, stable, easy to install, Bioperl inspired API
which I'd be happy to decorate to make more bioperl compatible via some
bridge, but forcing things through arbitary formats is straightforwardly

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