[Bioperl-l] Re: Bio::DasI

[Hilmar Lapp]

> -----Original Message-----
> From: bioperl-l-admin@bioperl.org 
> [mailto:bioperl-l-admin@bioperl.org]On
> Behalf Of Lincoln Stein
> Sent: Tuesday, May 21, 2002 12:48 PM
> To: Jason Stajich
> Cc: bioperl-l@bioperl.org
> Subject: [Bioperl-l] Re: Bio::DasI
> 
> 
> There's this interesting and unecessary dichotomy between the 
> entry-based 
> view of Bio::SeqI, which began life as a way to capture EMBL 
> entries, and the 
> landmark-based view of DasI, which began life as a way to 
> handle annotated 
> genomes.

I'd love to see these two views reconciled. The more I'm getting into making Biosql work for us, the more I'm concerned how this will play nice with the landmark view. The landmark view appears to call for blurring the bounday between bioentries and seqfeatures, whereas the biosql schema has strong differences between the two.

This is very relevant to us right now. What about a mini-hackathon with the key people in Edmonton? It'd be really great if after Edmonton or some time this summer there would be code and directions about how to resolve that dichotomy in Bioperl and Biosql. (I'm happy to contribute to that, in case this wasn't obvious. )

	-hilmar
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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