[DAS2] transitioning from DAS/1 to DAS/2
ap3 at sanger.ac.uk
Tue Dec 6 10:14:11 UTC 2005
> 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
> 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
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
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
> 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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