[Bioperl-l] Re: Bio::DasI

[Lincoln Stein]

On Thursday 23 May 2002 18:17, Hilmar Lapp wrote:
> > -----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.

BioSQL needs a robust Golden Path concept so that bioentries and seqfeatures 
can be transparently mapped onto the landmark-based view.  There are people 
working on these lines already, isn't that right?

>
> 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. )

If we put some serious time aside we might be able to accomplish something.  
I'm willing to do it during ISMB by sacrificing going to the sessions, but 
the consensus is that Edmonton isn't the best venue.

Lincoln