Hi Gabriel,
please let the datasetConfigVersion out or setting it to 0.6 or 0.7
means the same. hope this helps.
Best
Syed
On 26/08/2010 17:42, Richard Holland wrote:
I _think_ (not 100% certain) that doing this will get you the info you need:
http://www.biomart.org/biomart/martservice?type=configuration&dataset=btaurus_gene_ensembl
and look for the softwareVersion attribute in the DatasetConfig tag (very near
the top).
However I think the datasetConfigVersion in Query is not really that important
and I'm pretty sure it is never actually checked. Mostly it is checking that
the query format you are using is the same as the version of MartService you
are talking to - i.e. when talking to a 0.6 server, don't use any tags that
weren't introduced until 0.7, for instance.
But when all's said and done I'm not a huge BioMart expert at the moment so
I'll leave it to Syed and co. to correct me if I'm wrong!
cheers,
Richard
On 26 Aug 2010, at 17:01, Gabriel Berriz wrote:
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
--
Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holl...@eaglegenomics.com
http://www.eaglegenomics.com/
