[ensembl-dev] versioning of ensembl & biomart

[vincent ranwez]

Hi,

thank you very much for this answer. I tried to set the path to "http://www.ensembl.org/biomart/martservice?" but I got error message 'too many connection" it is thus probably wiser to wait a couple of days so that "http://www.biomart.org/biomart/martservice?" will be updated and ensembl server less loaded... Is there a way to know when this server is updated (apart from launching a request that give different result on ensembl v64 and v65) ?

Thank you again, I really appreciate the reactivity of the Ensembl team on this forum I think this is part of Ensembl success.

sincerely,

Vincent


Le 13 déc. 2011 à 13:53, Rhoda Kinsella a écrit :

> Hi Vincent
> In your webExample.pl script you are pointing to "http://www.biomart.org/biomart/martservice?" which should always point to the most recent Ensembl release. As it has only been a few days since the Ensembl release 65, the www.biomart.org central portal has not yet been updated to include the new databases. I expect that these will be updated some time this week. If you would like to use the Ensembl release 65 mart databases, you should set your path to "http://www.ensembl.org/biomart/martservice?" and then run your query. To obtain various archive releases, first determine the URL for the archive you wish to access using the following link:
> 
> http://www.ensembl.org/info/website/archives/index.html
> 
> If you select Ensembl release 63 from the list on the right hand side of the screen, and click on the BioMart link at the top of the page this will bring you to this URL:
> 
> http://jun2011.archive.ensembl.org/biomart/martview/
> 
> You can use this URL in the webExample.pl script if you modify the URL to have "/martservice?" at the end of the URL, like this:
> 
> http://jun2011.archive.ensembl.org/biomart/martservice?
> 
> This will allow you to query the Ensembl release 63 marts. I hope this helps but please don't hesitate to contact me if you have further questions.
> Regards
> Rhoda
> 
> 
> 
> On 13 Dec 2011, at 12:37, vincent ranwez wrote:
> 
>> 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");
>> 
>> 
>> 
>> _______________________________________________
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> 
> Rhoda Kinsella Ph.D.
> Ensembl Production Project Leader,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton
> Cambridge CB10 1SD,
> UK.
>