[Bioperl-l] GO annotatinos in BioPerl. A tentative proposal...

[Hilmar Lapp]

Ewan Birney wrote:
> >
> > What I propose to do is to create a new method of Feature objects,
> > $Feature->GO, which would set/return the GO annotation object associated
> > with that feature.  I would also modify the ->to_gff_string call such
> > that it checked for the presence of a GO annotation and dumped that
> > information into the GFF attributes field along with the other tag/value
> > information.
> 
> My approach would be this  (this is the "mix-in" type approach)
> 
>    Define an interface called
> 
>        Bio::GOContainerI
>           defines method ->each_GO();  # feel free to chose your own
> method.
> 
> The ->to_gff_string can test
> 
>     if( $seqfeature->isa('Bio::GOContainerI') ) {
>          # yadda yadda
>     }
> 
> Now make perhaps ::Gene object inheriet from Bio::GOContainerI as well as
> from Bio::SeqFeatureI.
> 

That's fine, too, but doesn't bring our Annotation object design
into shape :) (referring to what I just responded to Mark's
email).

	Hilmar
-- 
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Hilmar Lapp                              email: hilmarl@yahoo.com
GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
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