[BioC] ensembl biomart

[Sebastien Gerega]

BioMart seems to be down for me at the moment - can't even access 
http://www.biomart.org/news.html.
So out of curiosity I tried your code but got the following error.
 > listMarts(host="www.ensembl.org/biomart/martservice")
               biomart      version
1 ENSEMBL_MART_ENSEMBL   Ensembl 52
2     ENSEMBL_MART_SNP Variation 52
3    ENSEMBL_MART_VEGA      Vega 33
 > mart = useMart("ENSEMBL_MART_ENSEMBL", 
dataset="hsapiens_gene_ensembl", 
host="http://www.ensembl.org/biomart/martservice")
Error in file(file, "r") : cannot open the connection
In addition: Warning message:
In file(file, "r") : InternetOpenUrl failed: 'The URL is invalid'

Could you please tell me if I am doing something wrong.
thanks,
Sebastien

 > sessionInfo()
R version 2.8.0 beta (2008-10-05 r46601)
i386-pc-mingw32

locale:
LC_COLLATE=English_Australia.1252;LC_CTYPE=English_Australia.1252;LC_MONETARY=English_Australia.1252;LC_NUMERIC=C;LC_TIME=English_Australia.1252

attached base packages:
[1] splines   tools     stats     graphics  grDevices utils     
datasets  methods   base    

other attached packages:
 [1] biomaRt_1.16.0       GOstats_2.8.0        Category_2.8.1       
genefilter_1.22.0    survival_2.34-1      RBGL_1.18.0          
annotate_1.20.1    
 [8] xtable_1.5-4         graph_1.20.0         mouse4302.db_2.2.5   
GDD_0.1-13           annaffy_1.14.0       KEGG.db_2.2.5        
GO.db_2.2.5        
[15] RSQLite_0.7-1        DBI_0.2-4            AnnotationDbi_1.4.1  
limma_2.16.3         affyPLM_1.18.0       preprocessCore_1.4.0 
gcrma_2.14.1       
[22] matchprobes_1.14.0   affy_1.20.0          Biobase_2.2.1      

loaded via a namespace (and not attached):
[1] affyio_1.10.1   cluster_1.11.11 GSEABase_1.4.0  RCurl_0.92-0    
XML_1.94-0.1

steffen at stat.berkeley.edu wrote:
> That's indeed the default host as it is the central registry which keeps
> track of the available BioMarts and from there a dispatch happens to other
> hosts depending on the BioMart you use.
>
> You probably wanted to access the 52 version of Ensembl which is not yet
> available from biomart.org.  52 was released last week and it takes a few
> days to get that update into the central registry.
>
> Try this:
>
>   
>> listMarts(host="www.ensembl.org/biomart/martservice")
>>     
>                biomart      version
> 1 ENSEMBL_MART_ENSEMBL   Ensembl 52
> 2     ENSEMBL_MART_SNP Variation 52
>
>   
>> mart = useMart("ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl",
>>     
> host="www.ensembl.org/biomart/martservice")
>
>
> Cheers,
> Steffen
>
>   
>> 15/12/2008 17:09 Javier Díez scripsit
>>     
>>> Hi,
>>> Do you know how could I query the *martdb.ensembl.org* server, instead
>>> of
>>> the default server biomart.org ( I think this is the default server,
>>> isn't
>>> it?).
>>> Best
>>> Javi
>>>
>>>       
>> Have you tried typing
>>
>>  ? useMart
>>
>> and reading it?
>>
>>
>> The default value for 'host' is
>> "http://www.biomart.org/biomart/martservice"
>>
>> Best wishes
>>  Wolfgang
>>
>> ------------------------------------------------------------------
>> Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>>     
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>