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/
