[Bioperl-l] Re: [SO-devel] Re: GFF3 preliminary - NOW not NOT

[Richard Durbin]

Oops - yes I would NOW support.

Terrible typo!!!

Lincoln Stein wrote:
> Hi Richard,
> 
> 
>>PS If you are all working on this together, then my highest priority
>>plea is not to elevate start_codon and stop_codon to significant status.
>>  If you want to use endpoints then use interbase junctions
>>(coding_start and coding_end).  In fact I have wobbled backwards in the
>>great debate, and would not support Jim Kent and Lincoln to stick with
>>cds or (perhaps a better name) coding_exon regions joined together by a
>>common parent, as has been most widely used in earlier GFF and GTF.
> 
> 
> Could you clarify "and would not support Jim Kent and Lincoln..."?  I would 
> like to read this as a typo and infer that you "now" support Jim and myself.
> 
> Lincoln
> 
> 
>>Suzanna Lewis wrote:
>>
>>>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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>