[BioC] biomaRt: uniprot_mart

[James W. MacDonald]

Hi Nolwenn,

On 2/11/2011 10:19 AM, Le Meur-Rouillard, Nolwenn wrote:
> 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)  ?

Not familiar with the uniprot_mart, and you don't mention species. 
However, if your species isn't too exotic, can't you just use ensembl? 
For instance, the hsapiens_gene_ensembl lists these:

79            uniprot_sptrembl    UniProt/TrEMBL Accession
80           uniprot_swissprot        UniProt/SwissProt ID
81 uniprot_swissprot_accession UniProt/SwissProt Accession

Best,

Jim


>
> 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
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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