Hi Steve,
I don't really see the bifurcation between protein and genome DAS
that you mention. We use DAS/1 nicely for both genome and protein
clients.
Also the DAS/1 extensions have been designed with being able to work
with both worlds.
The real bifurcation I see is the geographical split between the US
and Europe as DAS is used in different ways here and there. Europe is
very much organized around DAS/1.
The ultimate goal of DAS is to separate data provision from
visualization. As such a goal for us all should be that a DAS source
can be shown in a similar fashion in all (genome) browsers. At the
present this is not possible. In order to achieve such a standard it
still will require a lot of collaboration, standardization and
convincing between the different client and server-providers.
Andreas
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 <[EMAIL PROTECTED]>
> Date: Thu, 27 Mar 2008 10:04:21 -0400
> To: Andreas Prlic <[EMAIL PROTECTED]>
> Cc: Steve Chervitz <[EMAIL PROTECTED]>, DAS/2 Discussion
> <[EMAIL PROTECTED]>, <[EMAIL PROTECTED]>
> 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 <[EMAIL PROTECTED]>
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 <[EMAIL PROTECTED]>
>>>> Date: Wed, 26 Mar 2008 16:01:26 +0000
>>>> To: <[EMAIL PROTECTED]>
>>>> 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
>>>> [email protected]
>>>> 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
>> [email protected]
>> http://lists.open-bio.org/mailman/listinfo/das
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