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

Chervitz, Steve Steve_Chervitz at affymetrix.com
Mon Jun 19 19:50:16 UTC 2006

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

  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

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

[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

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.

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