[BioC] problems connecting to Biomart today?

[Rhoda Kinsella]

Hi Jose,
The reason for this error is that the HGNC curated gene name attribute  
has been removed. We have also removed HGNC automated filters and  
attributes as these external references were confusing for users. You  
can still retrieve the HGNC ID and symbol and also the HGNC transcript  
name from the database. I hope this helps.
Regards
Rhoda


On 21 Feb 2011, at 12:19, <J.delasHeras at ed.ac.uk> wrote:

> I seem to be unable to use biomaRt today (working fine Friday) but I  
> don't see anything on the Biomart website wbout downtime, so I am  
> not sure if the problem lies at my end. Any ideas?
>
> Jose
>
> example:
>
> library(biomaRt)
> ensembl=useMart("ensembl")
> dataset="hsapiens_gene_ensembl"
> ensembl=useDataset(dataset, mart=ensembl)
>
> getBM(attributes="hgnc_curated_gene_name", filters="entrezgene",  
> values=c(1,33), mart=ensembl)
>
> I get:
> Error in getBM(attributes = "hgnc_curated_gene_name", filters =  
> "entrezgene",  :
>  Query ERROR: caught BioMart::Exception::Database: Could not connect  
> to mysql database ensembl_mart_61: DBI  
> connect('database=ensembl_mart_61;host=dcc-qa- 
> db.oicr.on.ca;port=3306','bm_web',...) failed: Can't connect to  
> MySQL server on 'dcc-qa-db.oicr.on.ca' (113) at /srv/biomart_server/ 
> biomart.org/biomart-perl/lib/BioMart/Configuration/DBLocation.pm  
> line 98
>>
>
>
> my sessionInfo()
>
> R version 2.11.0 (2010-04-22)
> i386-pc-mingw32
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United  
> Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C                            LC_TIME=English_United  
> Kingdom.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] xtable_1.5-6         GO.db_2.4.1          org.Hs.eg.db_2.4.1    
> annotate_1.26.0      GOstats_2.14.0
> [6] RSQLite_0.9-0        DBI_0.2-5            graph_1.28.0          
> Category_2.14.0      AnnotationDbi_1.10.1
> [11] Biobase_2.8.0        biomaRt_2.4.0
>
> loaded via a namespace (and not attached):
> [1] genefilter_1.30.0 GSEABase_1.10.0   RBGL_1.26.0        
> RCurl_1.4-2       splines_2.11.0    survival_2.35-9
> [7] tools_2.11.0      XML_3.1-0
>
>
> -- 
> Dr. Jose I. de las Heras                      Email: J.delasHeras at ed.ac.uk
> The Wellcome Trust Centre for Cell Biology    Phone: +44 (0)131  
> 6507095
> Institute for Cell & Molecular Biology        Fax:   +44 (0)131  
> 6507360
> Swann Building, Mayfield Road
> University of Edinburgh
> Edinburgh EH9 3JR
> UK
>
>
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.