[ensembl-dev] versioning of ensembl & biomart

[vincent ranwez]

Hi,

we are using XML biomart query (and a small perl script to launch this XML query) to collect some Ensembl information. I understand that there is distinct versioning of Ensembl and biomart, but I would like to know which Ensembl version is queried when using a XML query and  how to query peculiar version of Ensembl. It seems to me that my XML queries are done on Ensembl v64, is there a way to query v65 by modifying either the XML file (with the virtualSchemaName attribute ?) or the perl script (provided at the end of this mail).

Biomart web site provides an example to check default configuration : http://www.biomart.org/biomart/martservice?type=configuration&dataset=hsapiens_gene_ensembl but this does only provide the genome version and not the ensembl version. For instance this web page indicate that Homo sapiens genes (GRCh37.p5) is used but this is common to both version 64 and 65 of Ensembl that provide different results for simple query such as the list of human geneId and transcriptId (v64 178,538 results, v65 181,745). Moreover this does not explain how to use a specific configuration pointing toward a given Ensembl release.

I hope you can help me to solve this problem.

sincerely,

Vincent Ranwez


###################################
perl script use to run XML query files generated via ensembl web interface of biomart
###################################

use strict;
use LWP::UserAgent;


open (FH,"$ARGV[0]") || die ("\nUsage: perl webExample.pl Query.xml outupFile (pb with arg0)\n\n");
open (FILE,">>","$ARGV[1]") || die ("\nUsage: perl webExample.pl Query.xml outputFile (pb with arg1)\n\n");
close (FILE);

my $xml;
while (<FH>){
    $xml .= $_;
}
close(FH);

my $path="http://www.biomart.org/biomart/martservice?";
my $request = HTTP::Request->new("POST",$path,HTTP::Headers->new(),'query='.$xml."\n");
my $ua = LWP::UserAgent->new;

my $response;
my $tmp = "$ARGV[1]_tmp";
my $fileRes = $ARGV[1];;
$ua->request($request, "$tmp");
system("cat $tmp >> $fileRes; rm $tmp");