[DAS] Re: Protein DAS and C. elegans

[Julian Gough]

Lincoln,


> Discontinuous features simply have multiple <position> tags.  Both grouping 
> and the coordinate system itself is controlled by a <parent> href, which is 
> simply a local or remote URL.  This lets people attach subfeatures to 
> features referred to by other servers in a very RESTful manner.
> 
> How does this sound to you?  To Julian?

this sounds great. I actually suggested part of this myself in an
earlier E-mail to Tony. I think it makes a lot of sense, and is more
efficient.

Julian.


> 
> Lincoln
> 
> On Saturday 24 May 2003 03:58 am, Tony Cox wrote:
> > 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
> 
> -- 
> Lincoln Stein
> lstein at cshl.org
> Cold Spring Harbor Laboratory
> 1 Bungtown Road
> Cold Spring Harbor, NY 11724
> (516) 367-8380 (voice)
> (516) 367-8389 (fax)
> 
-- 
~~~~~~~~~~~~~~~~~~
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