[BioC] biomaRt query

[Rhoda Kinsella]

Hi Tim and Steffen,
You can also use the biomart attached to the http:// 
ncbi36.ensembl.org/ site using the following command:

 > mart = useMart("ENSEMBL_MART_ENSEMBL", host = "ncbi36.ensembl.org",  
dataset = "hsapiens_gene_ensembl")
Checking attributes ... ok
Checking filters ... ok

This mart is release version 54.
I hope that helps,
Regards,
Rhoda



On 16 Oct 2009, at 18:18, Steffen at stat.berkeley.edu wrote:

> Hi Tim,
>
> Do you specifically need Ensembl version 49 or would another Ensembl
> version using NCBI36 do?
>
> The error is probably generated because 49 is old and some changes  
> to the
> BioMart API occured after version 50 I think.  You can access  
> Ensembl 54
> which is also using NCBI36, by doing the following:
>
> ensembl 
> = 
> useMart 
> (host="may2009.archive.ensembl.org",biomart="ENSEMBL_MART_ENSEMBL",
> dataset="hsapiens_gene_ensembl")
>
> locations <- getBM(c('entrezgene','hgnc_symbol','chromosome_name',
> +                  'start_position','end_position'),  
> filters="entrezgene",
> +        values=entrezIDs, mart=ensembl)
>
>> locations
>  entrezgene hgnc_symbol chromosome_name start_position end_position
> 1      10857      PGRMC1               X      118254279    118262456
> 2       5055    SERPINB2              18       59689906     59722100
> 3       8334   HIST1H2AC               6       26232352     26292434
> 4       8349   HIST2H2BE               1      148080395    148124826
> 5      85236   HIST1H2BK               6       27214052     27222598
>
>
> Note that you can find the correct host names to use for specific  
> Ensembl
> versions by going to http://www.ensembl.org and then at the bottom  
> of the
> page, click on "view in archive site", select an archive and then  
> copy the
> url.
>
> Hope this helps,
> Steffen
>
>> Hi,
>>
>> I wanted to query on the NCBI36 build, and built the following query:
>> ----------------------------------------
>> entrezIDs <- c("8334","85236","10857","8349","5055") # sample list  
>> of ids
>>  ensembl <- useMart(biomart="ensembl",
>> dataset="hsapiens_gene_ensembl",archive=TRUE) #"ensembl_mart_49"
>>  locations <- getBM(c('entrezgene','hgnc_symbol','chromosome_name',
>>                 'start_position','end_position'),  
>> filters="entrezgene",
>>       values=entrezIDs, mart=ensembl)
>> _________________________________
>>
>>
>> I get the following error:
>> Error in listFilters(mart, what = "type") :
>>  The function argument 'what' contains an invalid value: type
>> Valid are: name, description, options, fullDescription, filters5,  
>> filters6
>>
>>
>> How should I modify the query? If I use the query with the current/ 
>> default
>> version of ensembl, the query executes ok.
>> thanks!
>> My sessionInfo() is:
>> -----------------
>> R version 2.9.1 (2009-06-26)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] grid      stats     graphics  grDevices utils     datasets   
>> methods
>> [8] base
>>
>> other attached packages:
>> [1] e1071_1.5-19        class_7.2-47        org.Hs.eg.db_2.2.11
>> [4] GOstats_2.10.0      graph_1.22.2        Category_2.10.1
>> [7] GO.db_2.2.11        biomaRt_2.0.0       multtest_2.1.1
>> [10] XML_2.5-3           genefilter_1.24.2   hgu133a.db_2.2.12
>> [13] RSQLite_0.7-1       DBI_0.2-4           AnnotationDbi_1.6.1
>> [16] GEOquery_2.8.0      RCurl_0.98-1        affy_1.22.0
>> [19] Biobase_2.4.1       gplots_2.7.1        caTools_1.9
>> [22] bitops_1.0-4.1      gdata_2.6.1         gtools_2.6.1
>> [25] lattice_0.17-25
>>
>> loaded via a namespace (and not attached):
>> [1] affyio_1.12.0        annotate_1.22.0      GSEABase_1.6.1
>> [4] MASS_7.2-47          preprocessCore_1.6.0 RBGL_1.20.0
>> [7] splines_2.9.1        survival_2.35-4      tools_2.9.1
>> [10] xtable_1.5-5
>>>
>>
>>
>>
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>>
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>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.