[Biojava-dev] Feature interface change

[Schreiber, Mark]

> -----Original Message-----
> From: Keith James [mailto:kdj@sanger.ac.uk] 
> Sent: Thursday, 22 August 2002 11:01 p.m.
> To: Matthew Pocock
> Cc: biojava-dev@biojava.org
> Subject: Re: [Biojava-dev] Feature interface change
> 
> 
> >>>>> "Matthew" == Matthew Pocock <matthew_pocock@yahoo.co.uk> writes:
> 
> [...]
> 
>     Matthew> Entities like genes or repeat types are realy first class
>     Matthew> objects. You could have all sorts of information attached
>     Matthew> to a Gene - phenotypes, diseases, all that biological
>     Matthew> stuff. You can have hierachies or ontologies of these
>     Matthew> terms. They realy exist independantly of any 'material
>     Matthew> view' on a bit of DNA sequence.
> 
> [...] interesting stuff snipped
> 
>     Matthew> Any thoughts anyone?
> 
> This is exactly the way that the GUS schema
> (https://sourceforge.net/projects/gusdev/) represents 
> annotation type data. I think it's a good idea. It also lets 
> you represent e.g. genes for which there is no sequence data 
> (but there is phenotype data or whatever).
> 
> Keith

It would make biojava less sequence centric which imho would be a good
thing. You could represent almost any kind of biological data this way,
mapping it to sequence if needed but also to experimental results,
literature searches etc.

How much breakage would occur to the biojava api? It would be good to
have this sooner rather than latter.

- mark
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