[DAS2] DAS/2 writeback

[Helt,Gregg]

But there's no entry in the segment query for chrI, which is the
chromosome you used in the the example XML you posted.  So I can't find
those annotations via IGB.
 
            gregg
 
-----Original Message-----
From: allenday at gmail.com [mailto:allenday at gmail.com] On Behalf Of Allen
Day
Sent: Monday, June 26, 2006 2:11 PM
To: Helt,Gregg
Cc: DAS/2
Subject: Re: DAS/2 writeback
 
This datasource contains both yeast and human segments.  I set it up
this way so features can be written for either human or yeast, then
viewed at one  of:

http://das.biopackages.net/das/genome/yeast/S228C-writeback/feature
http://das.biopackages.net/das/genome/human/17-writeback/feature

I thought this would be more useful so you can test viewing writeback
features alongside both "real" human and yeast features.

So you can just ignore the irrelevant segments, or if you'd prefer I can
delete one set of segments or the other.

-Allen


On 6/26/06, Helt,Gregg <Gregg_Helt at affymetrix.com> wrote:
Allen, thanks for getting the start of a writeback server up and
running!

I'm hoping to try writing back annotations later today.  However, I'm
having problems looking at the annotations in the writeback server via 
IGB.  It looks to me like the main issue is that
http://das.biopackages.net/das/genome/yeast/S228C-writeback/segment
returns human chromosome ids in the uri attribute of the SEGMENT 
element, instead of yeast ids.  When IGB uses this to compose a query
like

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

laps=chr1/10:15000;type=SO:centromere

it gets back an empty feature list.  But if I manually edit this to
replace "chr1" with "chrI",

http://das.biopackages.net/das/genome/yeast/S228C-writeback/feature?over
laps=chrI/10:15000;type=SO:centromere

I get back a list of feature that satisfies the query filters.

Any ideas?

        Thanks, 
        Gregg

> -----Original Message-----
> From: das2-bounces at lists.open-bio.org [mailto:das2-bounces at lists.open
-
> bio.org] On Behalf Of Allen Day
> Sent: Saturday, June 24, 2006 2:24 AM
> To: Chervitz, Steve
> Cc: DAS/2
> Subject: Re: [DAS2] Notes from the weekly DAS/2 teleconference, 19 Jun

> 2006
>
> 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-
<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
> >