[BioC] biomaRt: uniprot_mart

[Le Meur-Rouillard, Nolwenn]

Hi,

I need to re-run a 6 month-old chunk of code but I get an error with biomaRt when calling the uniprot_mart.:

" Incorrect BioMart name, use the listMarts function to see which BioMart databases are available"

A mart named unimart  seems to replace it (?)  but no dataset is attached to it.  Is the uniprot_mart deprecated or defunct, or it's a bug? What mart should I use to annotate Uniprot ID (protein name and functional annotation)  ?

Thanks
Nolwenn Le Meur



sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C

attached base packages:
[1] grid      stats     graphics  grDevices utils    
[6] datasets  methods   base     

other attached packages:
[1] biomaRt_2.6.0        xtable_1.5-6        
[3] ppiStats_1.16.0      ppiData_0.1.14      
[5] lattice_0.19-17      ScISI_1.22.0        
[7] apComplex_2.16.0     GO.db_2.4.5         
[9] RSQLite_0.9-4        DBI_0.2-5           
[11] RpsiXML_1.10.0       hypergraph_1.22.0   
[13] XML_3.2-0            annotate_1.28.0     
[15] AnnotationDbi_1.12.0 Biobase_2.10.0      
[17] RBGL_1.26.0          Rgraphviz_1.28.0    
[19] graph_1.28.0        

loaded via a namespace (and not attached):
[1] Category_2.16.0     GSEABase_1.12.2    
[3] RColorBrewer_1.0-2  RCurl_1.4-3        
[5] genefilter_1.32.0   org.Sc.sgd.db_2.4.6
[7] splines_2.12.1      survival_2.36-2    
[9] tools_2.12.1