[DAS] DAS workshop presentations

Andreas Prlic ap3 at sanger.ac.uk
Tue Apr 1 21:37:18 UTC 2008


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.
> >>>> _______________________________________________
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> >>>> 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.
> >>  _______________________________________________
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> >>  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

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 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 
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