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

[Lincoln Stein]

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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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
========================================================================