[DAS2] on local and global ids

Thomas Down td2 at sanger.ac.uk
Thu Mar 16 09:24:03 UTC 2006

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bandwidth reasons or b) they want to annotate an unpublished/new/ 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.)


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