[DAS2] on local and global ids

Lincoln Stein lstein at cshl.edu
Thu Mar 16 11:03:49 UTC 2006

I think it will help considerably to have a document that lists the valid 
sequence IDs for popular annotation targets. I've spoken with Ewan on this, 
and Ensembl will generate a list of IDs for all vertebrate builds. I'll take 
responsibility for creating IDs for budding yeast, two nematodes and 12 


On Thursday 16 March 2006 09:24, Thomas Down wrote:
> On 15 Mar 2006, at 21:25, Andrew Dalke wrote:
> > The problem comes when a site wants a local reference server.
> > These segments have concrete local names.
> >
> > DAS1 experience suggests that people almost always set up local
> > servers.  They do not refer to an well-known server.
> I'm not sure that DAS1 experience is a good model for this.  It's
> true that people didn't always point to well-known reference servers,
> but I think this has more to do with the fact that people didn't know
> which server to point to.  Some people did set up their own reference
> servers.  Many didn't, and many of those didn't give a valid
> MAPMASTER URL at all.  This situation didn't actually cause too much
> trouble since a lot of these users just wanted to add a track to
> Ensembl -- which doesn't care about MAPMASTER URLs and just trusts
> the user to add tracks that live in an appropriate coordinate system.
> I'd still argue that the majority -- probably the vast majority -- of
> people setting up DAS servers really just want to make an assertion
> like "I'm annotating build NCBI35 of the human genome" and be done
> with it.  That's what the coordinate system stuff in DAS/2 is for.
> If this is documented properly I don't think we'll see many "end-
> user" sites setting up their own reference servers unless a) they
> want an internal mirror of a well-known server purely for performance/
> bandwidth reasons or b) they want to annotate an unpublished/new/
> whatever genome assembly.
> (Actually, some of the "annotation providers set up their own
> reference servers" stuff might be my fault -- early versions of
> Dazzle were pretty strict about requiring a valid [and functional!]
> MAPMASTER for every datasource, so this pushed people towards setting
> up reference servers.)
>                  Thomas.
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Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
SANDRA MICHELSEN, AT michelse at cshl.edu (516 367-5008)

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