[Bioperl-l] Re: [SO-devel] Re: GFF3 preliminary

[Richard Durbin]

I have an edited version of SO which I will check back in shortly if it 
does not clash with too many other SO changes since Monday, in which the
SOFA:SOFA tags that Michael and I put in last week are replaced by 
either SOFA:junction or SOFA:region.  This makes explicit which SOFA 
terms are junctions and which are regions.

Note that SO/SOFA themselves don't mandate whether you use base 
coordinates (as in GFF) or interbase coordinates (as perhaps in some 
wizzy new format from Berkeley).  i.e. SO/SOFA are not formats, but 
ontologies of terms, and you can and should use them with other formats 
than GFF.  The distinction between regions and junctions is real 
however, and will have to be reflected in any format.  Some things 
inherently have extent covering bases (regions) and some things are 
boundaries between neighbouring bases (junctions).

Richard

Chris Mungall wrote:
> 
> On Fri, 21 Feb 2003, Richard Durbin wrote:
> 
> 
>>length
>>just before the start of the ATG and after the stop codon.  There are SO
>>terms for the start_codon and stop_codon but you really don't want to
>>use them to define the start and end.  e.g. Michael's 4 base start
>>codons, but also many start and stop codons are broken by introns.
>>There is no reason not to use junctions.
> 
> 
> Ah, ok - spaced on the distinction between codon/junction there
> 
> I'm still not comfortable with the hack to get round not having interbase
> coordinates, where certain subgraphs of SOFA are treated as flanking bases
> and the rest is treated as inclusive bases. I guess it's necessary for GFF
> though.
> 
> should we make this explicit in the names; eg all types for features have
> flanking-base coordinates have the suffix '_junction'?
> 
> 
>>Richard
>>
>>
>>
>>
> 
>