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

[seth redmond]

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

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