[DAS2] Notes from the weekly DAS/2 teleconference, 19 Jun 2006

[Allen Day]

You can see the features that are posted here:

http://das.biopackages.net/das/genome/yeast/S228C-writeback/feature

It is fully compatible with the usual yeast source:

http://das.biopackages.net/das/genome/yeast/S228C/feature

All the usual feature filters apply.  The response at this URL is not cached
to keep the content fresh, at the expense of ever-slower load times as
written features accumulate.

-Allen



On 6/24/06, Allen Day <allenday at ucla.edu> wrote:
>
> I have a temporary CGI set up to accept WRITEBACK documents:
>
> http://genomics.ctrl.ucla.edu/~allenday/cgi-bin/das2xml-parser/stable1.pl<http://genomics.ctrl.ucla.edu/%7Eallenday/cgi-bin/das2xml-parser/stable1.pl>
>
> I have attached a das2xml document that POSTs cleanly for me using the
> lwp-request that is part of libwww-perl.  Please modify this document, post,
> and let me know if anything breaks.
>
> This implementation accepts only new records.  It supports neither updates
> nor deletes.  Furthermore, it only accepts new feature records.  It does not
> support new type records, new region records, or any other type of record.
>
> Feature records may have 0 or more locations, 0 or more parents, 0 or more
> children, and 0 or more properties.  All parts/parents must be present in
> the document (no refering to existing features by URI), or it will throw a
> HTTP 500 error.
>
> Next I will implement the update and delete support.  This should be
> fairly straightforward, and may be doable over the weekend.
>
> -Allen
>
>
> On 6/19/06, Chervitz, Steve <Steve_Chervitz at affymetrix.com> wrote:
>
> > Notes from the weekly DAS/2 teleconference, 19 Jun 2006
> >
> > $Id: das2-teleconf-2006-06-19.txt,v 1.1 2006/06/19 19:48:57 sac Exp $
> >
> > Note taker: Steve Chervitz
> >
> > Attendees:
> >   Affy: Steve Chervitz, Ed Erwin, Gregg Helt
> >   UCLA: Allen Day
> >
> > Action items are flagged with '[A]'.
> >
> > These notes are checked into the biodas.org CVS repository at
> > das/das2/notes/2006. Instructions on how to access this
> > repository are at http://biodas.org
> >
> > DISCLAIMER:
> > The note taker aims for completeness and accuracy, but these goals are
> > not always achievable, given the desire to get the notes out with a
> > rapid turnaround. So don't consider these notes as complete minutes
> > from the meeting, but rather abbreviated, summarized versions of what
> > was discussed. There may be errors of commission and omission.
> > Participants are welcome to post comments and/or corrections to these
> > as they see fit.
> >
> > General announcements
> > ---------------------
> >
> > gh: We have received additional funding from NIH extending our support
> > through May 2007. This will provide us the support we need until the
> > new grant would kick in (the grant renewal we're planning to submit
> > Oct 2006). Many thanks to Peter Good who championed our cause at NIH.
> >
> > gh: considering moving das meeting to every two weeks, to get more
> > participation. we used to have alternating weeks -- one week focus on
> > spec, other week focus on implementations.
> >
> > [A] Gregg will broach possible biweekly das/2 meeting schedule on list.
> >
> > gh: Andrew is sick, so he won't be joining today.
> >
> > [Note: Last week only Steve, Gregg, and Ed E were on the call, so there
> > was no major DAS/2 discussion, hence no notes were posted.]
> >
> > Topic: Status reports
> > ---------------------
> >
> > gh: das2 writeback related work in IGB. can write back das2xml. can
> > make curations. options to save as bed or das2xml file. can make a
> > curation track, save as das2xml. there's an id resolution
> > issue. roundtripping works.
> >
> > Next step: make sure IGB can get back a das2 document that has same
> > xml with id mappings to different id. make sure I can swap
> > those. should then be able to writeback to a database.
> >
> > ee: improved sliced view in igb, shows where deleted exons have been
> > deleted. improved threading. slicing happens in a separate
> > interruptable thread. gff3 reading issue on the IGB forum, our parser
> > isn't gff3-ready.
> >
> > gh: deleted exons thing is cool. the gff parser is not fully
> > gff3-compliant.
> >
> > [A] Ed E. will fix gff3 parsing in IGB.
> >
> > ee/gh: implemented a speed up for drawing, min/max. once per pixel.
> >
> > sc: last development was on writing scripts to automate the updating
> > of the affy das/2 servers (dmz), so you can update the jars and
> > re-start the server.
> >
> > Other das-related stuff: Contributed to email discussion thread on the
> > W3C HCLS semantic web mailing list regarding "LSIDs in the wild",
> > provoked by Mark Wilkinson. Looks like about half a dozen or so places
> > that are using LSIDs in some capacity, but not a lot of resolution
> > services out there yet. Getting different data providers to use the
> > LSID syntax alone would be a big win. Asked Lincoln and Brian Gilman
> > about LSIDs at hapmap and caBIG (respectively). No response yet.
> >
> > Also responded to Ann's question on the das/2 list about using DAS to
> > look up genomic coords for a set of Entrez Gene ids. It would be nice
> > to have a way to determine the types of identifiers handled by a given
> > DAS server, so this sort of query could be handled automatically. If a
> > DAS server could provide a list of LSID authorities and namespaces for
> > the types of identifiers it can resolve, that could be used to provide
> > such a look up facility. This type of information could be provided to
> > the das/2 registry server at registration time.
> >
> > gh: yes, but not sure how to best deal with this information. possibly
> > via regular expressions on feature lookup, or xid.
> >
> > sc: Did other work related to Netaffx update preparation and domain
> > mapping project for exon array sequences, doing as collaboration with
> > Melissa Cline. Using Gregg's AnnotMapper.
> >
> > gh: will you provide data as RDF?
> > sc: it's still in flux, but possibly.
> >
> > gh: we were also going to talk about optimizing the data format for the
> > exon array as used on the affy das server, to deal with the growing
> > memory requirements. We can discuss this week.
> >
> > [A] Steve set up mtg with Gregg re: exon array data format for affy das
> > server.
> >
> > aday: working on updates to the biopackages das server.
> >
> > gh: is it ready to handle writeback requests?
> >
> > aday: will be by friday. can you handle different data sources? it's
> > in a separate db.
> > gh: as long as it's listed in sources query.
> > aday: it will be.
> >
> >
> >
> >
> >
> > _______________________________________________
> > DAS2 mailing list
> > DAS2 at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/das2
> >
>
>
>