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

[Ewan Birney]

On Thu, 5 Apr 2001, Chris Mungall wrote:

> > redesign the whole Annotation scheme. What I can see as for what
> > could make sense is
> > 
> > - Bio::AnnotationI as a minimum interface any sort of annotation
> > has to implement; this interface should provide for methods at
> > least sufficient to dump out the thing to GFF.
> > - Bio::Annotation::* to contain various implementations of that
> > interface tailored to specific types of annotation, with
> > - Bio::Annotation::GO being the one that represents a GO
> > annotation
> > - Bio::SeqFeatureI gets a method annotation() returning a
> > Bio::AnnotationI implementing object.
> > 
> > Right now, there is no AnnotationI interface, and classes in
> > Bio::Annotation are additions to an annotation object, not
> > specializations.
> 
> sounds good, although I am keen to see a seperation of the Annotation and
> the link between the feature and the Annotation, although minimal
> implementations of AnnotationI may choose to ignore that


I like this "audit trail" on annotation --- This is nice. Not sure if it
solves the how we tie annotations/features/whatevers together.


> 
> foreach $ann ($feature->annotations) {
> 
>   # minimal implementation
>   print $ann->description;
> 
>   # more useful:
>   printf "%s said that %s is a %s because\n",
>     $ann->association->person,
>     $feature->name,
>     $ann->controlled_vocab_term->description,
>     $ann->association->evidence_as_text;
> 
>   # association could be a 'null' object
>   # with 'unknown' in all the attributes
>   # for minimal implementations
> }
> 
> > 	Hilmar
> > -- 
> > -----------------------------------------------------------------
> > Hilmar Lapp                              email: hilmarl@yahoo.com
> > GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
> > -----------------------------------------------------------------
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> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> > 
> 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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