[DAS2] transitioning from DAS/1 to DAS/2

Andreas Prlic ap3 at sanger.ac.uk
Tue Dec 6 10:14:11 UTC 2005

Hi Andrew!

 > For at least a year I expect there will be both DAS/1 and DAS/2
 > servers.  We have or will have clients which can handle both
 > interfaces.
> I expect the metadata server should support both server types

I think there should be two different points where to get a list of 
DAS1 and DAS2 servers. after all it is
different protocols.

e.g. something like
das.sanger.ac.uk/registry/          ... the existing das1 registry
das.sanger.ac.uk/registry/das2/ ... the upcoming das2 registry.

> This means it must describe that data source "X" uses interface "A".
> I also expect that "A" can be:
>   - DAS/1 genomic annotations
>   - DAS/1.5 structure annotations

In terms of meta description, There is not much difference between 
genome, sequence and structure
  capabilities with DAS1. "structure" and "alignment" are just 2 
additional commands ("capabilities")
that a das server speaks (like "sequence" or "feature).  Still it is 
important to distinguish between the types of data.
Therefore the das1- registry style coordinate systems contain the 
information if the type is chromosomal,
protein sequence, or protein structure.

>   - DAS/2 genomic annotations
>   - DAS/2 protein annotations
>   - DAS/2 structure

this are the DAS2 - "domains" This leads to a discussion I would like 
to have next monday:

DAS1 is rather powerful, because it is possible to use the sequence and 
features commands
in a way that works for both genomic and protein sequences.  There is 
no need to distinguish between these
in the DAS1 - world.

I understand that one of the reason for creating the DAS2-"domains" is 
to have several "modules"  which can be
extended/developed independently. Still the genome -domain is very 
similar to what is needed for any kind of

I would therefore like to discuss to rename the "genome" domain to 

The information of which type of sequence, "genomic" or "protein 
sequence"  should be provided via the
source description.

> But we didn't talk about how to handle DAS/1 data sets in
> the metadata server.

if the source description is done well, it can also be used for das1 
servers. ( see my recent mail about
the "meta" description, which could be used like that for das1)

Something else I also would like to try is to provide a DAS2- proxy for 
DAS1 sources via the registry...
I.e. you can make a DAS2 request to a URL at the registry, which is 
translated to a DAS1 request
at the real server and then translated back again...


> -----------------------------------------------------------------------

Andreas Prlic      Wellcome Trust Sanger Institute
                               Hinxton, Cambridge CB10 1SA, UK
			 +44 (0) 1223 49 6891

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