[Bioperl-l] Bio::AnnotatableI function annotation()

Hilmar Lapp hlapp at gmx.net
Sat Mar 28 15:19:01 EDT 2009

On Mar 27, 2009, at 3:34 PM, Chris Fields wrote:

> I think there is still some contention about what the difference is  
> between a Feature and an Annotation.

A feature is (and in the BioPerl-way of looking at the world, should  
be) locatable, whereas annotation is not.

>  Our basic assumption is a Feature describes a specific section of  
> the sequence while Annotation describes the full sequence.

It depends on whether a piece of annotation is associated with the  
full sequence (i.e., the sequence object itself, or a feature object  
that happens to extend over the full length of the sequence), or with  
a feature at a specific location.

In principle, an annotation object is something that you would like to  
attach to an annotatable object (such as a feature). The reason you  
want to attach it (and any semantics implied by that reason) is in the  
tag. (Which is why there are in principle good reasons to have that  
tag come from an ontology.)


: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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