[DAS2] Human prototype server up
allenday at ucla.edu
Thu Apr 21 17:17:25 UTC 2005
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
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:
> 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?
> > -----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"
> > 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
> > There are no other applications on these hosts right now, so hammer
> > 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
> > is the feature/part subpart requests are done feature by feature due
> > the 1-many relationship... I'm still trying to figure out how to
> > 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
> > _______________________________________________
> > DAS2 mailing list
> > DAS2 at portal.open-bio.org
> > http://portal.open-bio.org/mailman/listinfo/das2
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