[BioSQL-l] Seqfeature_Source

[Hilmar Lapp]

> -----Original Message-----
> From: Thomas Down [mailto:td2@sanger.ac.uk]
> Sent: Monday, September 23, 2002 8:33 AM
> To: Hilmar Lapp
> Cc: biosql-l@open-bio.org
> Subject: Re: [BioSQL-l] Seqfeature_Source
> 
> 
> On Mon, Sep 23, 2002 at 12:42:25AM -0700, Hilmar Lapp wrote:
> > >
> > >How do you plan to do this?  I can think of three possibilities:
> > >
> > >  - Have a standard tag for seqfeature_source, and then put
> > >    the source value (as a string) in the current
> > >    seqfeature_qualifier_value table.  I don't have any particular
> > >    objections to this, but it's got the same problem as putting
> > >    the source as a text attribute in the main seqfeature
> > >    table: it leaves the source as an opaque string.
> > 
> > Why is the string in seqfeature_source so different from this?
> 
> It's normalized.

That's true. If it were an ontology_term (the source term itself), it would be normalized too. 

<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?

> 
> 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