[Open-bio-l] RE: [GMOD-devel] RE: Schema for genes & features & mappings to assemblies

[Hilmar Lapp]

> -----Original Message-----
> From: Lincoln Stein [mailto:lstein@cshl.org]
> Sent: Thursday, April 25, 2002 12:00 PM
> To: Hilmar Lapp; Elia Stupka; Thomas Down
> Cc: Ewan Birney; GMOD Devel (E-mail); OBDA BioSQL (E-mail)
> Subject: Re: [GMOD-devel] RE: Schema for genes & features & 
> mappings to
> assemblies
> 
> 
[...]
> 
> > Aggregation on the software layer is one way of
> > implementing a view on the model; sadly enough MySQL 
> completely dismissed
> > the concept of models and views, but with Oracle you can 
> implement any view
> > you want in the database layer.
> 
> Chris demonstrated the utility of views very nicely in his 
> last letter, IMO.

Absolutely.

> 
> > What we (we refering to our group here) will need for 
> assemblies is to
> > represent existing ones such that we can stick in all the 
> mappings (of
> > features, genes, markers, etc). I thought that would then 
> underpin all
> > mapped entities with a sequence; i.e., in order to obtain a 
> feature's
> > sequence you need to specify the feature /and/ the assembly 
> (assuming you
> > have a mapping for that assembly); this means a gene's CDS 
> sequence is
> > going to be different from one assembly to another. The 
> open question is
> > whether r not you still need a fixed sequence for that 
> feature (e.g., in
> > order to map it). Does this make some sense or sound like a 
> stupid idea?
> 
> I don't understand this one.  If you've annotated a CDS on 
> one assembly, and 
> a second assembly changes the underlying sequence, is it 
> valid to map the CDS 
> from one assembly onto the new one?  Surely you would rather want to 
> reannotate that area and call a new CDS.
> 

I guess I wasn't clear (and probably I'm still not a 100% clear) myself what I need to do and how, so some of my thoughts are rather undistilled. The scenario I had in mind was along the following lines: you have a RefSeq gene and map it to different assemblies. If you are confident in RefSeq genes, you could then call the mapped regions genes by definition; the sequence then associated with those genes may differ (e.g., exons missing etc) between assemblies and between assemblies and the RefSeq entry. Nonetheless, I agree you would re-map for a new assembly.

	-hilmar
-- 
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Hilmar Lapp                            email: lapp@gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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