[BioSQL-l] Seqfeature_Source

[David Block]

On Monday, September 23, 2002, at 10:05  AM, Hilmar Lapp wrote:
> <snip>
>>
>> <change_of_subject />
>>
>> Thinking a bit more generally about your changes to BioSQL, and issues
>> you discussed at BOSC, I've noticed some overlap with the ways we're
>> talking about handling annotated sequence in BioJava2.  The basic plan
>> is to separate features (which might be genes, or other objects) from
>> their mappings onto sequences.  All the type information, and
>> most (all)
>> of the key-value stuff (which will hopefully be more strongly
>> constrained
>> by the type system) goes onto the FeatureCard, while the
>> FeatureMapping
>> stays very simple.  It allows you to build a system which gives
>> equal weight to `gene-centric' and `sequence-centric' views of
>> your annotation (unlike BioJava1, which turns out very strongly
>> sequence-centric).
>
> This sounds very interesting. Dave, hear this? That's what we want 
> isn't it?

Yep.  That's about what I'm building as EJBeans and adaptors for Apollo.

I guess I'll take another look at BioJava as well.
>
>>
>> I don't know if there's any enthusiasm at all for building this
>> kind of pattern into the next generation of BioSQL.
>
> Why not? But then I'm saying this without having seen what you guys 
> dream of ...
>
> OK, so you're saying I should resume my biojava-l subscription?
>
> 	-hilmar
>
--
David Block                                  dblock@gnf.org
GNF - San Diego, CA             http://www.gnf.org
Genome Informatics / Enterprise Programming
Weblog:      http://radio.weblogs.com/0104507/