[ensembl-dev] BioMart Ensembl version

[Guillermo Marco Puche]

Dear Thomas,

My BioMart perl script is using the following mart XML config file:

<?xml version="1.0" encoding="UTF-8"?>

<!DOCTYPE MartRegistry>

<MartRegistry>

     <MartURLLocation

         name         = "ensembl"

         displayName  = "ensembl"

         host         = "www.biomart.org"

         port         = "80"

         visible      = "1"

         default      = ""

         includeDatasets = "hsapiens_gene_ensembl"

         martUser     = ""

     />

</MartRegistry>

However, I'm getting BioMart queries from hg19 and not hg38. Does the 
default port '80' still working on hg19? how can I specify I would like 
to use hg38 biomart service.

On the other hand, it's always useful to know how to query older Ensembl 
versions with Biomart. However using $action=clean with conf file of 
ensembl 75 archive it's leading me to massive amounts of RAM consumption 
in my Perl script.

Thanks.

Best regards,
Guillermo.
On 19/09/14 15:48, Thomas Maurel wrote:
> Dear Guillermo,
>
> If you are using:
> 1) the biomart-perl/scripts/webExample.pl script and an xml file
> You can change the path to the biomart website in the following line:
>
>     my $path="http://www.biomart.org/biomart/martservice?";
>
> With the path to our Ensembl release 75 archive:
>
>     my $path="http://feb2014.archive.ensembl.org/biomart/martservice?";
>
>
> 2) A BioMart perl script
> a) You first need to edit your configuration file in 
> "biomart-perl/conf/martURLLocation.xml" and paste the content of the 
> mart registry page for the Ensembl release 75 archive website: 
> http://feb2014.archive.ensembl.org/biomart/martservice?type=registry
> b) Then edit your script and make sure that "my $confFile" variable is 
> looking at the martURLLocation.xml configuration file in biomart-perl/conf
> c) Finally, make sure to update the following line in your script:
>
> my $action='cached';
>
> with:
>
> my $action='clean';
>
> The first run of your script on Ensembl 75 might be a bit slow as 
> BioMart will cache some data from the BioMart website.
> Once you have run your script with the action variable set to "clean", 
> you can set the variable to "cached" again.
>
> Hope this helps,
> Best regards,
> Thomas
> On 19 Sep 2014, at 13:28, Guillermo Marco Puche 
> <guillermo.marco at sistemasgenomicos.com 
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
>> Dear developers,
>>
>> I would like to know how to specify BioMart Perl code to query 
>> against older Ensembl version (ie:75) and not latest (I believe used 
>> by default).
>>
>> Thank you.
>>
>> Best regards,
>> Guillermo.
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>
> --
> Thomas Maurel
> Bioinformatician - Ensembl Production Team
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
>
>
>
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