[ensembl-dev] versioning of ensembl & biomart

vincent ranwez vincent.ranwez at univ-montp2.fr
Wed Dec 14 10:16:43 GMT 2011


I launch my script this morning on your server and it works fine except for the tasmania devil. Indeed the orthology field for this species does not use the same convention as other species :
<Dataset name = "hsapiens_gene_ensembl" interface = "default" >
		<Attribute name = "ensembl_gene_id" />
		<Attribute name = "ensembl_transcript_id" />
		<Attribute name = "devil_ensembl_gene" />
		<Attribute name = "homolog_shar__dm_description_4014" />
		<Attribute name = "cat_ensembl_gene" />
		<Attribute name = "cat_orthology_type" />
		<Attribute name = "chimp_ensembl_gene" />
		<Attribute name = "chimp_orthology_type" />
So I have to make a special case for this species. This is a minor problem, but I was wondering if it has a special meaning (i.e. less reliable prediction of the homology ?)

thanks for your help,


Le 14 déc. 2011 à 09:05, rhoda at ebi.ac.uk a écrit :

> Hi Vincent
> Unfortunately, someone has been hitting our mart servers with a lot of
> queries over the past few days and we are trying to resolve the
> connectivity issue. Can you try your query again today and let me know if
> you can retrieve your results? You will need to keep an eye on
> www.biomart.org to determine when this is updated with the new release 65
> databases or perhaps you could subscribe to the biomart users mailing list
> (users at biomart.org). The BioMart team are generally quite quick to update
> these databases once we have added them to the public mysql server and
> they usually let me know when they have been added to the biomart central
> portal. I then email the biomart users mailing list and bioconductor
> mailing list to let everyone know about the fixes and additions in the new
> marts. I hope that helps.
> Regards
> Rhoda
>> 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");
>>>> _______________________________________________
>>>> Dev mailing list    Dev at ensembl.org
>>>> List admin (including subscribe/unsubscribe):
>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>> Ensembl Blog: http://www.ensembl.info/
>>> Rhoda Kinsella Ph.D.
>>> Ensembl Production Project Leader,
>>> European Bioinformatics Institute (EMBL-EBI),
>>> Wellcome Trust Genome Campus,
>>> Hinxton
>>> Cambridge CB10 1SD,
>>> UK.

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