A compare/contrast document on DAS1/2 would be great. On a different note ---
Does anyone know if the Gbrowse/GMOD system includes a DAS service? -Ann On Tue, Apr 1, 2008 at 9:03 PM, Steve Chervitz <[EMAIL PROTECTED]> 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. > > [ 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 <[EMAIL PROTECTED]> > > Date: Tue, 1 Apr 2008 22:37:18 +0100 > > To: Steve Chervitz <[EMAIL PROTECTED]> > > Cc: DAS/2 Discussion <[EMAIL PROTECTED]>, <[EMAIL PROTECTED]> > > > > 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 <[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 > >>>> > >> This transmission is intended for the sole use of the individual > >> and entity to whom it is addressed, and may contain information > >> that is privileged, confidential and exempt from disclosure under > >> applicable law. You are hereby notified that any use, > >> dissemination, distribution or duplication of this transmission by > >> someone other than the intended addressee or its designated agent > >> is strictly prohibited. If you have received this transmission in > >> error, please notify the sender immediately by reply to this > >> transmission and delete it from your computer. Thank You. > >> Affymetrix, Inc. > > > > ----------------------------------------------------------------------- > > > > 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. > > > ------------------------------------------------------------ > > > This transmission is intended for the sole use of the individual > and entity to whom it is addressed, and may contain information > that is privileged, confidential and exempt from disclosure under > applicable law. You are hereby notified that any use, > dissemination, distribution or duplication of this transmission by > someone other than the intended addressee or its designated agent > is strictly prohibited. If you have received this transmission in > error, please notify the sender immediately by reply to this > transmission and delete it from your computer. Thank You. > Affymetrix, Inc. > > > _______________________________________________ > DAS2 mailing list > [EMAIL PROTECTED] > http://lists.open-bio.org/mailman/listinfo/das2 > _______________________________________________ DAS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/das
