[Biojava-dev] Feature interface change

[Schreiber, Mark]

> -----Original Message-----
> From: Thomas Down [mailto:td2@sanger.ac.uk] 
> Sent: Friday, 23 August 2002 1:25 a.m.
> To: Matthew Pocock
> Cc: biojava-dev@biojava.org
> Subject: Re: [Biojava-dev] Feature interface change
> 
> Since we're talking about revolution rather than evolution 
> here , I wonder 
> if it might not also be time to reconister the 1-to-many 
> relationship we currently have between parent and child 
> features.  As a first step:
> 
> 
>     public interface FeatureCard extends BJ2Identifiable {
>         public FeatureType getType();
>         public Set<FeatureMapping> getFeatureMappings();
>         public Set<FeatureCard> getChildren();
>         public Set<FeatureCard> getParents();      
>     }
> 
> A more extreme option would be to generalize things 
> completely and just have `relationships' between features, 
> and an (extensible) voccabulary of relationship types.  This 
> is done in the post-cape-town BioSQL schema, although I don't 
> know of anything which really takes advantage of it yet.  
> It's interesting, but we should probably look for use-cases 
> before deciding.
> 

I favour the extreme option as long as the ontology of the relationships
is well constructed. It would help ease us away from the sequence
centricity.

- Mark

Mark Schreiber
Bioinformatics
AgResearch Invermay
PO Box 50034
Mosgiel
New Zealand
 
PH:   +64 3 489 9175
FAX:  +64 3 489 3739

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