[DAS2] Notes from DAS/2 code sprint #3, day three, 16 Aug 2006

Lincoln Stein lstein at cshl.edu
Thu Aug 17 16:01:18 UTC 2006

What's the conference call number?


On 8/16/06, Steve Chervitz <Steve_Chervitz at affymetrix.com> wrote:
> Notes from DAS/2 code sprint #3, day three, 16 Aug 2006
> $Id: das2-teleconf-2006-08-16.txt,v 1.1 2006/08/16 17:05:24 sac Exp $
> Note taker: Steve Chervitz
> Attendees:
>   Affy: Steve Chervitz, Ed E., Gregg Helt
>   Dalke Scientific: Andrew Dalke
>   UCLA: Allen Day, Brian O'Connor
> 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.
> Topic: Spec Q&A
> ---------------
> bo: perusing spec, saw mention of XID as a filter. can I get more
> explanation?
> ad: can't remember without looking at docs, but think I was not sure
> what XID was supposed to be, lincoln sent email to clarify.
> aday: an external db id trying to resolve into local space, eg., for gene
> das.
> ad: don't think there was enough info there to be useful.
> gh: just uri and nothing else?
> ad: looking at steve's notes from 16 march. looks like we deferred it.
> gh: input was minimal. I have no particular use for it.
> bo: need to know what support to provide for the biopackages server.
> in the read spec, says "it's not well though-out. should have
> authority, type, id, description."
> bo: type vs. exact type
> gh: did we get rid of exact type?
> ad: see gregg's email from 16 march:
> http://lists.open-bio.org/pipermail/das2/2006-March/000655.html
> The assumption was, there's no type inferencing done on the
> server. it's just done on the client. we were to rename 'exacttype' to
> 'type' and use exacttype semantics for it.
> gh: there is no parent-child structure to types. there is to ontology
> though.
> ad: type records in das aren't parent-child relations because they
> combine other info about type, e.g., ways to depict it.
> bo: looking for places where our server disagreed with spec. segments
> feature filter is not supported on our end. overlaps segments. but
> this is just work we need to do, not a spec issue.
> gh: allen and lincoln were struggling with xml:base resolution yesterday,
> looking through the xml:base spec, dealing with edges. are you satisfied?
> aday: yes
> gh: for implementes that don't already deal with xml:base resoultion,
> it may take a day or so to deal with it. nomi and I struggled as
> well. I was suprised it is not so supported in xml libraries.
> ad: just a matter of walking up the xml tree.
> gh: recursively had to verify that the resolve stuff in the java
> networking libraries actually worked according to the xml:base spec.
> but we've moved through this.
> bo: url example, uses 'segment' and 'sequence'. not so consistent.
> gh: pros and cons to this. it shows that das/2 links can be built
> using different uris.
> ad: used different url structures to show that this was possible.
> bo: confusing when you only see a snippet and don't see where the uri
> was coming from. showing variety is useful though.
> gh: are both specs frozen now?
> ad: yes.
> Topic: Status Reports
> -----------------------
> bo: went through spec. updated our bug queue. added bug re: passing in
> id filters vs. uris. working on this today.
> aday: need to resolve type ids, need to deal with relative ids given
> in the document. now can go back to working on writeback.
> gh speaking for lincoln: perl stuff for gbrowser to connect to das
> servers. went through xml:base abyss.
> updated uris for sequence and genome version ids for human and mouse
> on the wiki page: http://open-bio.org/wiki/DAS:GlobalSeqIDs
> sc: should we allow anyone to edit this, of just lincoln?
> gh: would like to restrict it. worried about wiki graffiti.
> ad: you have to register. we can always back things out.
> sc: lincoln will get notification upon any edits.
> gh: ok.
> gh: working on igb release. adding parsing abilities. can now focus on
> das/2, mostly writeback stuff, refining that in igb client.
> ee: finishing up bugfixes before igb release. will start on gff3
> parser today.
> ad: looked into content negotiation stuff. why validator server on
> open-bio site isn't working: I updated underlying webserver
> framework. working on that.
> sc: worked on creating new data files used by the affy das server for
> exon arrays using gregg's new parser.
> gh: this is generating more efficient versions of probe sets for exon
> arrays. important since the affy das server is in-memory.
> sc: this will help us support more arrays in the das server and also
> move away from having to maintain two different das servers, so we can
> focus on just the das/2 server.
> sc: also working on final touches on web page describing available data on
> our das servers.
> gh: we can modify xml from the server to point at that page as an info
> url. sources element has info url, and sub elements as well, but we
> can just put the info page at the top level.
> sc: also was working on ann's fly data project, where she needs to
> pull genomic regions relative to probe sets. we need to update our
> das alignment file (link.psl) to be based on dm2.
> gh: we don't provide residues. she'll have to do a das/1 query at ucsc
> to get residues.
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Lincoln D. Stein
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)
SANDRA MICHELSEN, AT michelse at cshl.edu

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