[DAS2] /das/assay namespace

[Allen Day]

is available for browsing on the prototype server.  example queries:

http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest
http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/algorithm
http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/assay
http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/material
http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification

These are more interesting:

#get quantification 2753.  it's a netCDF file of a HG-U133A chip 
#quantified/normalized with Bioconductor's GCRMA algorithm
http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification/2753

#as above, but use a feature filter from genome-das to only retrieve 
#measurements from 10-90Mb on chrY.
http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification/2753?feature.overlaps=chrY/10000000:90000000;algorithm=3

#as above, but retrieve 10-90Mb on chrY for all GCRMA-processed chips, of
#which there are 661.
http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification?feature.overlaps=chrY/10000000:90000000;algorithm=3

#as above, but restrict to CNS samples instead of all 661.  this 
#filter doesn't work yet.
http://das.biopackages.net/das/assay/chado/chado-Hsa-17-allenday-gectest/quantification?feature.overlaps=chrY/10000000:90000000;algorithm=3;material.type=MA:central_nervous_system

In principle, any feature filter can be used with the /quantification
request by simply prefixing with "feature." to enable passthru to the
feature filter classes on the server.  In practice, none of the Affymetrix
probesets are annotated with anything beyond their region and primary type
of SO:PCR_product, so the only interesting filters to use deal with
coordinates.

It could be interesting to start attaching the Affymetrix probeset
annotations from NetAffx, so you could e.g. retrieve genome-wide
expression of RTKs for all CNS samples, without having to perform overlap
queries to get to the annotations on the mRNA that are being assayed...  

I'm almost happy with my prototype -- I'll turn it into a spec document
soon.

-Allen