[DAS2] DAS/2 weekly meeting notes for 14 Nov 05

[Thomas Down]

On 14 Nov 2005, at 19:29, Steve Chervitz wrote:
>
> Coord system reg server:
> * in das/2 - it's not optional (0 interbase)
> * they find this important

By "coordinate system" we're not really talking about the 0-based- 
vs-1-based issue, we're talking about globally unique names for sets  
of reference sequences (genome assemblies, protein databases,  
whatever).  It might be possible to come up with a better name (I  
used to call these "namespaces").

> We have confusion between assembly and reference server
> LS: Need URI that points to assembly, independent of the
> reference server.
> GH: Would like to have annot servers that don't know anything about
> the ref server

Definitely agree with this.  This kind of "opaque assembly  
identifier" is what we've been calling a coord-system name.

> LS: Could use the region URI to ID the assembly
> das/genome/sourceid/region = assembly id/uri
>
> GH: The trouble is that NCBI is a ref source for many assemblies, yet
> they lack a das sever. They have no URI.
> LS: we can just make one up, or use most appropriate web page

This is possibly an argument for avoiding the use of URLs for  
assembly identifiers, if we can't be sure that the organisation  
that's the authority for a given assembly will be running an  
authoritative DAS server.  URNs would be fine, as would the kind of  
structured but location-independent identifer that Andreas has been  
using.

> Question: What do they mean by 'coord system'? some confusion here
> e.g., Do they mean things like: 'this assembly start at 5000 relative
> to this other assembly'?

I think the way to provide this kind of information is in the form of  
a DAS alignment service between two coord-systems.  We love the idea  
of putting up alignments between NCBI34 and NCBI35 then having a  
liftover-like tool which can go off and query the registry to  
discover this.

           Thomas.