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 <[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.
_______________________________________________
DAS mailing list
[email protected]
http://lists.open-bio.org/mailman/listinfo/das
_______________________________________________
DAS mailing list
[email protected]
http://lists.open-bio.org/mailman/listinfo/das
