On 100826T, at 10:08, Richard Holland wrote:
On 100813F, at 16:30, Gabriel Berriz wrote:
Is there a programmatic way to get the correct value of the
datasetConfigVersion attribute, for queries like
<!DOCTYPE Query>
<Query completionStamp="1" count="" datasetConfigVersion="0.6"
requestId="biomart-client" uniqueRows="1"
virtualSchemaName="default">
<Dataset interface="default" name="btaurus_gene_ensembl">
<Attribute name="ensembl_gene_id" />
<Attribute name="description" />
</Dataset>
</Query>
btaurus_gene_ensembl is a dataset name, not a mart name. The
parameter 'mart' requires a mart name. In this case (admittedly I
did this by process of guessing) the mart name for the mart that
contains the dataset btaurus_gene_ensembl is 'ensembl'.
Hi. Thanks for the correction.
Therefore the following works the way you are probably expecting it
to:
http://www.biomart.org/biomart/martservice?mart=ensembl&type=version
When I visit this URL, I get the value 0.6, but the BioMart
documentation (p. 68) suggests that the value for the
datasetConfigVersion attribute should be at least 0.7:
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query virtualSchemaName = "default" uniqueRows = "" count = ""
datasetConfigVersion = "0.7" >
<Dataset name = "mytest" interface = "default" >
<Attribute name = "ensembl_transcript_id" />
<Attribute name = "chromosome_name" />
<Filter name = "chromosome_name" value= "22"/>
</Dataset>
</Query>
I'm not sure how to make sense of this.
My goal here is to find a programmatic way to determine the most
current value for the datasetConfigVersion attribute.
If anyone knows how to do this, please let me know.
TIA!
Gabriel
=============================================================
Gabriel F. Berriz, PhD
Senior Bioinformatics Developer
Roth Lab
Biological Chemistry and Molecular Pharmacology -- Harvard Medical
School
250 Longwood Avenue
Seeley G. Mudd Building 322B
Boston, MA 02115-5701
Telephone: 617.432.3555
Fax: 617.432.3557
