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

[Suzanna Lewis]

Hi Richard,

Looks like you committed your changes to so.ontology and I
committed changes to sofa.ontology. Michael, Chris, and I
are here in Chicago together and we'll try to work on
resolving the Singapore changes to sofa back into so proper.
Not sure where the differences will be, but it will be
interesting I'm sure. Chris has added some definitions
as well for sofa which should help in revealing what our
thinking was.

-S


On Friday, February 21, 2003, at 04:21 AM, Richard Durbin wrote:

> 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
>>>
>>>
>>>
>>>
>
>
>
>
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