[DAS2] Human prototype server up

[Allen Day]

This is a good region.  I just realized the type ids coming back in the
/type response don't match the type ids given in the /feature response.  
I'm in the process of switching over from using table PKs for types to
using type names, so rather than using a filter "type=9770" you can
instead us a filter "type=sofa.ontology:CDS" (the "sofa.ontology" string
is the term's namespace.  SO has already changed it to "SOFA" in their
most recent SOFA file in CVS, but I haven't updated yet).

So, sorry about that.  I just change thed /type response back to give
primary keys until I get names working.  All the types should now work
with the type= filter.  Here's a quick document you can grab, a subregion
of what you asked for in your request that has something interesting
inside:

http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlaps=chr21/21292691:21324284;type=9688

-Allen



On Thu, 21 Apr 2005, Helt,Gregg wrote:

> Cool, great to see a public server up and running!
> 
> However, I'm having trouble with feature queries.  For example:
> http://das.biopackages.net/das/genome/chado/chado-Hsa-17/feature?overlap
> s=chr21/21500000:22500000;type=0000110
> 
> Which is an example of the most typical query IGB will be making -- one
> overlap filter combined with one type filter.  But this query returns
> with a single <FEATURELIST> line, no <FEATURES>.  I've tried it for
> every type returned by the type query and get the same results.
> 
> Is there something wrong with my query syntax?  
> 
> If this is not a good region to test, can you send me an example feature
> query URL where you know what the response should be?
> 
> 	thanks!
> 	gregg
> 
> > -----Original Message-----
> > From: das2-bounces at portal.open-bio.org
> [mailto:das2-bounces at portal.open-
> > bio.org] On Behalf Of Allen Day
> > Sent: Wednesday, April 20, 2005 10:42 PM
> > To: das2 at portal.open-bio.org
> > Subject: [DAS2] Human prototype server up
> > 
> > Contains UCSC Hg17 knownGene, as well as all Affymetrix "target"
> sequences
> > aligned to the genome w/ > 90% identity.
> > 
> > http://das.biopackages.net/das/genome/chado/chado-Hsa-17/region
> > 
> > Here's a URL to get you going.  This is running on 2 hosts: a dual
> > opteron/8GB webserver frontend and a dual opteron/16GB database
> backend.
> > There are no other applications on these hosts right now, so hammer
> away.
> > 
> > You might want to use HTTP 1.1 keepalive though, the responses can be
> > *really* slow for /feature requests on large regions.  The reason for
> this
> > is the feature/part subpart requests are done feature by feature due
> to
> > the 1-many relationship... I'm still trying to figure out how to
> improve
> > this.
> > 
> > Components that aren't working in even a basic way:
> > 
> >   * alignments
> >   * assemblies
> >   * individual /feature/<id> requests
> >   * versioned source response w/ supported formats
> >   * most feature filters (overlaps, type, and exacttype work)
> > 
> > -Allen
> > _______________________________________________
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> > DAS2 at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/das2
>