[BioC] biomaRt

[James W. MacDonald]

And to expand on this a bit further, you don't have to use the default 
biomart server. For instance, if biomart.org is down, you could 
presumably use the biomart server that Ensembl has set up.

As I am in the US, my local ensembl server is uswest.ensembl.org, so

 > listMarts(host="uswest.ensembl.org", path="/biomart/martservice")
                biomart                        version
1 ENSEMBL_MART_ENSEMBL               Ensembl Genes 58
2     ENSEMBL_MART_SNP           Ensembl Variation 58
3 ENSEMBL_MART_FUNCGEN Ensembl Functional Genomics 58
4    ENSEMBL_MART_VEGA                        Vega 38
5             REACTOME                       Reactome
6          wormbase195         WormBase 195 (CSHL US)
7                pride                 PRIDE (EBI UK)

 > mart <- useMart("ENSEMBL_MART_ENSEMBL", "hsapiens_gene_ensembl", 
host="uswest.ensembl.org", path="/biomart/martservice")
Checking attributes ... ok
Checking filters ... ok>

Note that the ensembl server is a bit more schizophrenic than the 
biomart server, so if you get an error like this, then you may need to 
try again:

 > mart <- useMart("ENSEMBL_MART_ENSEMBL", "hsapiens_gene_ensembl", 
host="uswest.ensembl.org", path="/biomart/martservice")
Checking attributes ...Error in bmAttrFilt("attributes", mart) :
   biomaRt error: looks like we're connecting to incompatible version of 
BioMart suite.

I got this error directly after a successful connection, so there you go.

 > getBM(c("affy_hg_u133_plus_2", "entrezgene"), "affy_hg_u133_plus_2", 
"1007_s_at",mart)
   affy_hg_u133_plus_2 entrezgene
1           1007_s_at        780
2           1007_s_at         NA

Best,

Jim



On 7/13/2010 2:17 PM, Steve Lianoglou wrote:
> Hi Fraser,
>
> On Tue, Jul 13, 2010 at 1:19 PM, James W. MacDonald
> <jmacdon at med.umich.edu>  wrote:
>> No, I am not talking about your internet connection, I am talking about the
>> biomart web server at http://www.biomart.org/. The biomaRt package by
>> default uses this web server, so if you cannot get the page to load in a
>> browser, you will not be able to query using biomaRt either.
>
> I think some people get confused and think the biomart service is
> something owned/operated by the bioconductor folks: it's not.
>
> As Jim points out, the web server is here:
> http://biomart.org
>
> The bioconductor package "biomaRt" is simply an R library that calls
> out to the biomart.org service with well-formed URL's that are built
> by the criteria constructed in your getBM (or whatever) function
> calls.
>
> If biomart.org is down, then your getBM calls will also fail, but
> there's nothing that can be done about that on this list. Probably
> your best bet is to contact the biomart.org people directly.
>
> That having been said, it seems that biomart.org is back up now.
>
> Hope that clears things up (if they needed clearing to begin with :-).
>

-- 
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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