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

[Jim Kent]

Yea!

cds may not be the greatest name, but it is common usage
already, so let's stick with it.

----- Original Message -----
From: "Richard Durbin" <rd at sanger.ac.uk>
To: <lstein at cshl.org>
Cc: <song-devel at lists.sourceforge.net>; "Chris Mungall" <cjm at fruitfly.org>; <gff-list at sanger.ac.uk>;
<bioperl-l at bioperl.org>; <michele at sanger.ac.uk>
Sent: Thursday, March 06, 2003 3:12 AM
Subject: Re: [SO-devel] Re: GFF3 preliminary - NOW not NOT


> 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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