[DAS] DAS workshop presentations
Ewan Birney
birney at ebi.ac.uk
Wed Apr 2 07:28:01 UTC 2008
On 2 Apr 2008, at 02:03, Steve Chervitz wrote:
> 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.
>
One important thing in my mind is that "writeback" is a really huge
additional concept that carries so many semantic issues which many
servers
just cannot implement (for sure, Ensembl is not going to be implementing
a writeback server in the near term).
For me, DAS's sweet spot is a "dumb server, smart client" mode, where
there a few clients and many servers, and servers are easy to put up
etc. Write back requires smart(er) servers.
So I would also advocate splitting the DAS/2 discussing into "read-only"
and "read-write" scenarios. I know this is implicitly there but I would
argue worth formalising at a higher level, and would stress the servers
can still be dumb.
It is also worth noting that DAS/1 has evolved as a "de facto", working
standard around the hinxton campus and we've really made good use and
built up momentum around it. It takes a long time bizarrely for people
to pick up technology and use it, and I want to make sure DAS/2
discussion doesn't scare the growing set of people picking up and using
DAS/1 - which is very useful, pragmatic and critically has working
servers and clients now.
> [ 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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