[ensembl-dev] Ensembl Plant Biomart

Dan Staines dstaines at ebi.ac.uk
Wed Jun 17 16:28:29 BST 2015


On 17/06/15 12:34, Jonathan MELIUS wrote:
> Dear all,
>
> Is the plant biomart service down ? The martview is working fine. But
> when I try to use the martservice I have one error:
>
>> Problem retrieving attributes for dataset  in schema , check your parameters
>
> I try the examples on http://plants.ensembl.org/biomart/martservice too:
>>
>> - to retrieve attributes available for a dataset:http://plants.ensembl.org/biomart/martservice?type=attributes&datatset=atauschii_eg_gene
>> - to retrieve filters available for a dataset:http://plants.ensembl.org/biomart/martservice?type=filters&datatset=atauschii_eg_gene
> Still the same error.

It appears that the martservice documentation page you found is out of 
date, and I suspect its not maintained any more as we use an older 
version of BioMart. I'll look into fixing this. By the way, can I ask 
how you found that page?

You need to add the mart or virtualSchemaName (which come from the 
registry):
e.g.
http://plants.ensembl.org/biomart/martservice?type=attributes&mart=plants_mart_27&dataset=atauschii_eg_gene
http://plants.ensembl.org/biomart/martservice?type=filters&mart=plants_mart_27&dataset=atauschii_eg_gene

> I'm also wanted to know if it is possible, like with the main website,
> to query a previous release:
> e.g http://oct2014.archive.ensembl.org/biomart/
> <http://oct2014.archive.ensembl.org/biomart/martservice >martservice
> <http://plants.ensembl.org/biomart/martservice> -> Ensembl 77
>
> Or in the query, I just have to put the "virtualSchemaName" on
> "plants_mart_26" not 27 ?

No, we only maintain one release on our public mart servers, but our 
public MySQL server contains mart databases from the last 10 releases 
which you should be able to point your own martservice/API code at.

Hope that helps,

Dan.

-- 
Dan Staines, PhD               Ensembl Genomes Technical Coordinator
EMBL-EBI                       Tel: +44-(0)1223-492507
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/




More information about the Dev mailing list