[DAS] DAS workshop presentations

Wed Apr 2 01:03:21 UTC 2008

You're right. The bifurcation that has me concerned is really:

DAS/1 --> genome & protein
DAS/2 --> genome only

Though DAS/2 can be used for protein sequence annotations, it has so far
mainly (only?) been used for serving genome annotations. The retrieval DAS/2
spec itself is very genome-centric and could be updated/generalized to
include protein examples.

So I guess it's not so much a bifurcation but a disparity in level of
support and usage patterns that distinguishes the 1 vs 2 versions of the
spec, and this disparity seems destined to ensure the co-existence
incompatible DAS 1 & 2 clients and servers.

DAS/1 has a large installed base of servers and clients and the DAS/1 spec
has more extensive support for protein sequence annotations.

DAS/2 has some enhancements including support for alternative formats and an
incipient writeback (annotation editing) facility. Usage as so far been
confined to genome browsers.

[ BTW: there isn't a good document describing these DAS/2 enhancements and
how DAS/2 diverges from DAS/1. I'll try and put something up on the
biodas.org wiki about this. In the meantime, there is a brief summary here:
http://biodas.org/documents/das2/das2_protocol.html ]

I agree with your ultimate goal for DAS. Getting there will take some
effort, but promoting that vision is a important step. Resuming the
conference calls as Ann mentioned will help.

Cheers,
Steve

> From: Andreas Prlic <ap3 at sanger.ac.uk>
> Date: Tue, 1 Apr 2008 22:37:18 +0100
> To: Steve Chervitz <Steve_Chervitz at affymetrix.com>
> Cc: DAS/2 Discussion <das2 at lists.open-bio.org>, <das at biodas.org>
> Subject: Re: [DAS] DAS workshop presentations
> 
> 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 <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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> 
> -----------------------------------------------------------------------
> 
> 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. 

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