[DAS] Re: Protein DAS and C. elegans

[Tony Cox]

Lincoln,

I think feature linking by ID is common becasue it is (a) the simplest thing
to do from the drawing code point of view and (b) because it is not
obvious/clear how to manipulate the <TARGET> and  <GROUP> tag contents and
attributes when loading data into an LDAS server.

Maybe it would be nice to add another data field to allow the explicit
setting of the <GROUP> and/or <TAGET> tags - or indeed any of the other tags
down there in the FEATURE object that may be useful like <NOTE>.

> Lincoln,
>
> this is indeed what I am doing, and I very much welcome the move to
> modify the spec to allow this explicitly (from what I can make out it
> isn't disallowed anyway).
> However I feel that I have to make absolutely clear what Tony said about
> it because I think I have been ever so slightly misunderstood.

I don't know how....

> So far as
> I can recall from what Tony said no other Protein DAS server is doing
> this, only mine, but he said "We routinely use same IDs to 'link'
> features into a structure.... If Ensembl encounters a list of exon
> features all with the same ID it groups them into a transcript." I think
> perhaps referring to non-protein DAS.

Look Julian, I don't draw a distinction between "protein DAS", "non-protein
DAS" or any other perceived 'flavour' of DAS.  It is all about serving
annotations on a sequence. Proteins are not a special case. Grouping by
feature ID is simply expedient whether it is to link exons in DNA or domains
on a swissprot sequence. The main thing is that the spec is able to allow
people to get their data out there easily and not bog them down in semantic
quicksand.

Tony

>
> Anyway I'm sure you'll get the full story from him.
>
> Julian.
>
> On Sat, 2003-05-24 at 07:18, Lincoln Stein wrote:
> > Hi Tony,
> >
> > Julian tells me that the various protein DAS servers are serving domains
that
> > are on discontinuous regions of the genome by giving each feature the
same
> > feature ID rather than linking them by using the same group.  This
strategy
> > makes sense, and is in fact what the GFF3 spec calls for, but isn't what
the
> > DAS/1 spec says.  The question is:
> >
> > - How widespread is this practice?  Should I modify the 1.X spec
> > retrospecticely to allow it?
> >
> > Lincoln
> >
> > -- 
> > ========================================================================
> > Lincoln D. Stein                           Cold Spring Harbor Laboratory
> > lstein at cshl.org                   Cold Spring Harbor, NY
> > ========================================================================
> >
> -- 
> ~~~~~~~~~~~~~~~~~~
> Julian Gough
> Department of Structural Biology
> School of Medicine, Fairchild bldg D109
> Stanford University, CA 94305-5126, U.S.A.
> Tel: +1 650 7250754
> Fax: +1 650 7238464