Here are a few notes about DAS/2 activity: The DAS/2 retrieval spec for genome annotations has been stable and considered ready for production use since Nov 2006: http://biodas.org/documents/das2/das2_get.html
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. _______________________________________________ DAS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/das
