[DAS] Fwd: [DAS2] DAS/2 specification problems

[Gregg Helt]

Heh, after posting asking people to make sure they crosspost to DAS and
DAS/2 lists until the lists merge, of course I'm finding posts that I forgot
to crosspost!  Here's one that's relevant to the URI resolvability issues
being discussed in a current thread:

---------- Forwarded message ----------
From: Gregg Helt <gregghelt at gmail.com>
Date: Wed, Oct 15, 2008 at 10:46 AM
Subject: Re: [DAS2] DAS/2 specification problems
To: "Nicol, John" <John.Nicol at uncc.edu>
Cc: das2 at lists.open-bio.org


Apologies, most of the XML responses in the DAS/2 protocol specification are
only examples, not responses from actual servers.  We could change this so
that the spec uses example from working servers.  However, none of the
currently deployed DAS/2 servers that I know of exercise every optional
element and attribute of the spec, so they would be incomplete examples.
But the spec HTML docs are definitely due for an overhaul...

Here's the overview page for the main Affymetrix DAS/2 server, with example
sources, types, segments, and features queries:
    http://netaffxdas.affymetrix.com/das2

Also, at least one of the URLs you list is not guaranteed to be resolvable:
http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B34.3/dna/chr4
This is given as the value for the uri attribute of a COORDINATES element.
These URIs MAY be resolvable but do not have to be.

In general as part of a spec revision (DAS 2.1?) I'd like to eliminate more
of the resolvability requirements in the specification, and specify that
most URIs be used as identifiers with _optional_ resolvability.  After two
years of working with the current spec I've come to believe that for most
cases requiring URI resolution is not necessary, places added burden on
server implementations, and limits the ability to do non-authoritative
decentralized annotation.

     sincerely,
     Gregg


On Tue, Oct 14, 2008 at 11:36 AM, Nicol, John <John.Nicol at uncc.edu> wrote:

> Hi all,
>
> I'm looking at the DAS/2 specification (at, say,
> http://biodas.org/documents/das2/das2_get.html), and I'm encountering some
> problems.
>
> Specifically, none of the biodas links appear to work.  These would be
> useful to do some verifications on our server.
> http://www.biodas.org/das/sequence/gallus_gallus/March2004/types
> http://www.biodas.org/known_das_servers
> http://www.biodas.org/sequence/s.cerevisiae/genes.xml
>
> Many of the other links don't work.  For example:
> http://dev.wormbase.org/das/genome/  (which itself links to the unknown
> http://www.biodas.org/das2)
> http://www.ensembl.org/Homo_sapiens/Chr1
> http://das.ensembl.org/das/SPICEDS/127/
> http://sanger.ac.uk/das-registry/yeast-32-chromosome
> http://flybase.org/genome/D_melanogaster/R4.3/dna/X
> http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B34.3/dna/chr4
>
> And here's a typo:
> http://ensemble.org/Homo_sapiens/Chr1
>
> Thanks!
> John
>
>
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