[ensembl-dev] entrez gene IDs missing on protist biomarts?

[Dan Staines]

Hi Seth,

Thanks for reporting this - we're looking into this right now, and will 
let you know when we have a solution.

Thanks for your patience,

Dan.

On 01/09/2012 09:19 PM, seth redmond wrote:
> Have sent this to the list once, but it didn't get a reply and it isn't
> showing up in the archives, so I'll try again:
>
> I'm trying to do a biomaRt query and I seem to be throwing errors on
> protists_mart_12 that weren't there in protists_mart_10.
> In particular 'entrezgene' has disappeared from berghei, and is present
> in falciparum:
>
>> >
>> subset(listAttributes(useMart("protists_mart_12",dataset="pfalciparum_eg_gene")),name=="entrezgene")
>> name description
>> 28 entrezgene EntrezGene ID
>> >
>> subset(listAttributes(useMart("protists_mart_12",dataset="pberghei_eg_gene")),name=="entrezgene")
>> [1] name description
>> <0 rows> (or 0-length row.names)
> Attempting to run a query (falciparum, entrezgene) on martview suggests
> it's been removed from the mart schema, but not from the front-end (see
> error message below). I don't think I see anything in the release notes
> about removing entrezgenes, so is this likely to be fixed before next
> release?
>
> thanks
>
> -s
>
>
>
>> Serious Error: Error during query execution: Unknown column
>> 'protists_mart_12.pfalciparum_eg_gene__ox_entrezgene__dm.translation_id_1068_key'
>> in 'where clause'
>>
>> ERROR: caught BioMart::Exception::Database: Error during query
>> execution: Unknown column
>> 'protists_mart_12.pfalciparum_eg_gene__ox_entrezgene__dm.translation_id_1068_key'
>> in 'where clause'
>>
>> If you repeatedly get directed to this error page, there may be a
>> problem with your current session parameters. To clear your session
>> and start with a clean slate, please click the *New* button below.
>>
>> Stacktrace:
>> Exception::Class::Base::throw
>> /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/Dataset/TableSet.pm:241
>> BioMart::Dataset::TableSet::_fillAttributeTableWith
>> /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/Dataset/TableSet.pm:124
>> BioMart::Dataset::TableSet::_getResultTable
>> /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/DatasetI.pm:1170
>> BioMart::DatasetI::getResultTable
>> /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/QueryRunner.pm:472
>> BioMart::QueryRunner::_processPath
>> /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/QueryRunner.pm:374
>> BioMart::QueryRunner::_getResultTable
>> /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/QueryRunner.pm:194
>> BioMart::QueryRunner::execute
>> /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/Web.pm:2429
>> (eval)
>> /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/lib/BioMart/Web.pm:2197
>> BioMart::Web::handle_request
>> /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/cgi-bin/martview:107
>> (eval)
>> /net/isilonP/public/rw/ensembl/ensembl-genomes/release-12/biomarts/protists/biomart-perl/cgi-bin/martview:106
>> ModPerl::ROOT::ModPerl::Registry::net_isilonP_public_rw_ensembl_ensembl_2dgenomes_release_2d12_biomarts_protists_biomart_2dperl_cgi_2dbin_martview::handler
>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
>> (eval)
>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:204
>> ModPerl::RegistryCooker::run
>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/RegistryCooker.pm:170
>> ModPerl::RegistryCooker::default_handler
>> /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/ModPerl/Registry.pm:31
>> ModPerl::Registry::handler -e:0
>> (eval) -e:0
>>
>
>
>
> --
> Seth Redmond
> Unité de Genetique et Genomique des Insectes Vecteurs
> Institut Pasteur
> 28,rue du Dr Roux
> 75724 PARIS
> seth.redmond at pasteur.fr <mailto:seth.redmond at pasteur.fr>
>
>
>
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-- 
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/