[Bioperl-l] Re: [Bioperl-announce-l] an extension to Bio::SeqIO

Ewan Birney birney at ebi.ac.uk
Tue Jun 17 23:58:23 EDT 2003

On Tue, 17 Jun 2003, Lincoln Stein wrote:

> Hi,
> Once I hear that there's a more-or-less consensus on the GFF3 spec that I sent
> out, I'll make the appropriate changes to Bio::SeqIO to support it.  The
> important features are:

I think this list of features is great:

> 	- ontology-based types & relationships

  - great.

> 	- parentage relationships are independent of position relationships

  - I really like this.

> 	- multiple parents

  - not 100% keen, but still ok

> 	- split locations

  - I doubt we will kill them ever. So, they stay.

> 	- separation of group from ID

  - great

> 	- arbitrary attributes (but they can be constrained by a CV if need be)

  - great.

> I think this will go a long way toward making Jason's Transmogrifiers easier
> to write, and help with chado roundtripping.

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