[BioC] ensembl biomart

[James W. MacDonald]

Hi Sebastien,

I don't get the same error, but I am also unable to connect. However, 
using the MySQL interface does appear to work:

 > listDatasets(useMart("ensembl_mart_52", mysql=T))
connected to:  ensembl_mart_52
                           dataset        version
1           aaegypti_gene_ensembl         AaegL1
2           agambiae_gene_ensembl         AgamP3
3            btaurus_gene_ensembl         Btau_4
4           celegans_gene_ensembl          WS190
5        cfamiliaris_gene_ensembl        BROADD2
6      cintestinalis_gene_ensembl           JGI2
7         cporcellus_gene_ensembl        cavPor3
8          csavignyi_gene_ensembl        CSAV2.0
9      dmelanogaster_gene_ensembl        BDGP5.4
10     dnovemcinctus_gene_ensembl           ARMA
[snip]

Best,

Jim



Sebastien Gerega wrote:
> 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
>>
>>
> 
> _______________________________________________
> 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

-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662