[DAS2] [DAS] DAS workshop presentations

Tue Apr 1 01:51:46 UTC 2008

Here are a few notes about DAS/2 activity:

The DAS/2 retrieval spec for genome annotations has been stable and
considered ready for production use since Nov 2006:
http://biodas.org/documents/das2/das2_get.html

There are perhaps are a handful of sites in the U.S. that have (or are
planning to) deploy DAS/2 servers in production environments, though I don't
have any official numbers. We've been tracking them here:
http://www.biodas.org/wiki/DAS/2#DAS.2F2_Servers

Since the DAS/2 retrieval spec stabilized, there has been some work on the
writeback portion of the spec (for creating/editing annotations), but that
has not been finalized. As far as I know, it hasn't progressed since the
original grant for DAS/2 spec development ended in Oct 2007. There was some
good work done on the writeback spec as well as some early implementations
and it would be good to see it congeal eventually.

I know there's been continued development of the DAS/1 spec:
http://www.dasregistry.org/spec_1.53E.jsp

This has stirred up some thoughts I've been chewing on recently regarding
where DAS is headed. Comments welcome. Here goes:

While it would be nice to see a single DAS spec to simplify the lives of
people writing clients and to unite development efforts, I wonder if this is
reasonable expect yet. The genome vs. protein annotation bifurcation that we
have now may reflect a natural division that might be difficult to unite
into a single spec. However, I think the current state is more a matter of
the large amount of inertia behind DAS/1 -- the shear number of existing
DAS/1 servers and DAS/1 client code out there -- coupled with the fact that
DAS/2 is not backward compatible. Code doesn't rewrite itself.

I know one of the early roadblocks for getting protein annotation support
into DAS/2 was that protein features were not described by the Sequence
Ontology (SO), but this has since been rectified. I've learned that since
August 2007, all of the protein features in the bioSapiens project have been
incorporated into SO ( http://www.dasregistry.org/extension_ontology.jsp ).

The DAS/1 -> DAS/2 proxy adapter that Andrew Dalke worked on (
http://lists.open-bio.org/pipermail/das2/2006-October/000268.html ) could
help with DAS/2 migration. But that project never fully matured. Continued
development of DAS/1 could complicate the development of such an adapter.

Regarding the genome-vs-protein DAS split, certainly there are many
commonalities at the level of annotations along a linear sequence which
apply equally well to nucleotide and protein sequences. Maybe it would help
to have a partitionable DAS spec to separate core things from extensions
that are nucleotide or protein-specific? This could help isolate the more
stable, low-level things from higher-level functionality that is specific to
nucleotide or protein sequences, and could evolve without impacting the core
spec. A given DAS server would be compliant with the core and either the
genome or protein specific extensions of the spec.

Cheers,
Steve 

> From: Ann Loraine <aloraine at gmail.com>
> Date: Thu, 27 Mar 2008 10:04:21 -0400
> To: Andreas Prlic <ap3 at sanger.ac.uk>
> Cc: Steve Chervitz <Steve_Chervitz at affymetrix.com>, DAS/2 Discussion
> <das2 at lists.open-bio.org>, <das at biodas.org>
> Subject: Re: [DAS] DAS workshop presentations
> 
> Regarding the funding issue:
> 
> NSF is awarding me some funds that will support developing a
> Distributed Annotation Server to use for Arabidopsis data. (It is
> through the 2010 program.)
> 
> DAS is not the main focus of the grant, but will play a big part in what we
> do.
> 
> I am also working on arranging a number we could use to carry on the
> DAS conference calls.
> 
> Previously they were hosted by Affymetrix, but I think we can probably
> do this for the group here at Charlotte. (I'm at University of North
> Carolina Charlotte.)
> 
> All the best,
> 
> Ann
> 
> On Thu, Mar 27, 2008 at 9:35 AM, Andreas Prlic <ap3 at sanger.ac.uk> wrote:
>> Hi Steve,
>> 
>>  We did not have an "official" slot for DAS/2, partially because we
>>  did not have any DAS/2 related speakers. In the informal discussions
>>  some concern re DAS/2 was raised,
>>  particularly about backwards compatibility issues and regarding
>>  whether DAS/2 is still active and funded.
>> 
>>  Cheers,
>>  Andreas
>> 
>> 
>> 
>> 
>>  On 27 Mar 2008, at 01:24, Steve Chervitz wrote:
>> 
>>> Thanks Andreas. Looks like you had a good workshop.
>>> Was there any discussion pertaining to DAS/2?
>>> 
>>> Steve
>>> 
>>>> From: Andreas Prlic <ap3 at sanger.ac.uk>
>>>> Date: Wed, 26 Mar 2008 16:01:26 +0000
>>>> To: <das at biodas.org>
>>>> Subject: [DAS] DAS workshop presentations
>>>> 
>>>> Hi,
>>>> 
>>>> We recently were hosting a DAS workshop at the Genome Campus in
>>>> Hinxton, U.K..
>>>> 
>>>> In case you are interested, the presentations of the first day (DAS -
>>>> client developers day) are available from:
>>>> http://www.dasregistry.org/course.jsp
>>>> 
>>>> The slides used for the second day (hands-on) are available from:
>>>> http://www.biodas.org/wiki/DASworkshop200802
>>>> 
>>>> Cheers,
>>>> Andreas
>>>> 
>>>> ---------------------------------------------------------------------
>>>> --
>>>> 
>>>> Andreas Prlic      Wellcome Trust Sanger Institute
>>>>                                Hinxton, Cambridge CB10 1SA, UK
>>>>                                +44 (0) 1223 49 6891
>>>> 
>>>> ---------------------------------------------------------------------
>>>> --
>>>> 
>>>> --
>>>>  The Wellcome Trust Sanger Institute is operated by Genome Research
>>>>  Limited, a charity registered in England with number 1021457 and a
>>>>  company registered in England with number 2742969, whose registered
>>>>  office is 215 Euston Road, London, NW1 2BE.
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>> 
>> 
>>  -----------------------------------------------------------------------
>> 
>>  Andreas Prlic      Wellcome Trust Sanger Institute
>>                                Hinxton, Cambridge CB10 1SA, UK
>>                                +44 (0) 1223 49 6891
>> 
>>  -----------------------------------------------------------------------
>> 
>> 
>> 
>> 
>>  --
>>   The Wellcome Trust Sanger Institute is operated by Genome Research
>>   Limited, a charity registered in England with number 1021457 and a
>>   company registered in England with number 2742969, whose registered
>>   office is 215 Euston Road, London, NW1 2BE.
>>  _______________________________________________
>>  DAS mailing list
>>  DAS at lists.open-bio.org
>>  http://lists.open-bio.org/mailman/listinfo/das
>> 

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