[BioC] Biomart server down?

Fri May 20 17:35:32 CEST 2011

Is it possible to download? For example:

Filters Feature Type :
      RegulatoryFeature
Attributes:
      Feature Set
      Feature Type
      Chromosome Name
      Start (bp)
      End (bp)

On Fri, May 20, 2011 at 5:18 PM, Rhoda Kinsella <rhoda at ebi.ac.uk> wrote:
> Hi Fabrice
> Unfortunately we have never been able to have a functional count for the
> regulation mart as restrictions in the 0.7 Biomart code as well as the
> complexity of the regulation schema does not allow it. The rest of the mart
> does work as expected.
> Regards
> Rhoda
>
>
> On 20 May 2011, at 16:08, Fabrice Tourre wrote:
>
>> On website
>> http://www.ensembl.org/biomart/martview/a711f46360c68acaec88385696d09186/a711f46360c68acaec88385696d09186
>>
>> I want to get the REGULATORY FEATURES
>>
>> It seems not work.
>>
>> Dataset Count unavailable
>>
>>
>> On Fri, May 20, 2011 at 4:58 PM, Rhoda Kinsella <rhoda at ebi.ac.uk> wrote:
>>>
>>> Hi Alistair
>>> You can set your host to www.ensembl.org and use the Ensembl Biomart
>>> databases there.
>>> Regards
>>> Rhoda
>>>
>>>
>>> On 20 May 2011, at 15:44, Alistair Rust wrote:
>>>
>>>> Hi,
>>>>
>>>> I've had an R script playing nicely with biomaRt for a while
>>>> Today there seem to be a few wee problems.  Is the result
>>>> of the server being down in Toronto?
>>>>
>>>> SessionInfo, a simple test and output below.  I downloaded
>>>> and installed the 2.8.0 version of biomaRt this morning.
>>>> Also tried the 2.9.0 development version with the same
>>>> results.
>>>>
>>>> Cheers
>>>>
>>>> Alistair
>>>>
>>>> Team113: Experimental Cancer Genetics,
>>>> Wellcome Trust Sanger Institute,
>>>> Hinxton, Cambridge, UK
>>>>
>>>>
>>>>> sessionInfo()
>>>>
>>>> R version 2.11.1 (2010-05-31)
>>>> x86_64-unknown-linux-gnu
>>>>
>>>> locale:
>>>> [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>>>> [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>>>> [5] LC_MONETARY=C              LC_MESSAGES=C
>>>> [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>>>> [9] LC_ADDRESS=C               LC_TELEPHONE=C
>>>> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>>>>
>>>> attached base packages:
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>> other attached packages:
>>>> [1] biomaRt_2.8.0
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] RCurl_1.4-2 XML_3.1-0
>>>>
>>>>
>>>> Simple test from the R script on the BioConductor biomaRt webpage
>>>> ========
>>>> library(biomaRt)
>>>>
>>>> listMarts()
>>>>
>>>> ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
>>>>
>>>> affyids=c("202763_at","209310_s_at","207500_at")
>>>>
>>>> getBM(attributes=c('affy_hg_u133_plus_2', 'entrezgene'), filters =
>>>> 'affy_hg_u133_plus_2', values = affyids, mart = ensembl)
>>>> =========
>>>>
>>>>
>>>>
>>>> Output
>>>> =========
>>>>
>>>>    V1
>>>>
>>>> 1 <!DOCTYPE html PUBLIC -//W3C//DTD HTML 4.01//EN
>>>> http://www.w3.org/TR/html4/strict.dtd>
>>>> 2
>>>> <html><head>
>>>> 3                        <meta http-equiv=Content-Type
>>>> content=text/html;
>>>> charset=utf-8>
>>>> 4                         <title>ERROR: The requested URL could not be
>>>> retrieved</title>
>>>> 5                                                             <style
>>>> type=text/css><!--
>>>> 6
>>>> /*
>>>> Error in getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"),
>>>> filters
>>>> = "affy_hg_u133_plus_2",  :
>>>>  The query to the BioMart webservice returned an invalid result: the
>>>> number
>>>> of columns in the result table does not equal the number of attributes
>>>> in
>>>> the query. Please report this to the mailing list.
>>>>
>>>>       [[alternative HTML version deleted]]
>>>>
>>>> _______________________________________________
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>>>
>>> Rhoda Kinsella Ph.D.
>>> Ensembl Bioinformatician,
>>> European Bioinformatics Institute (EMBL-EBI),
>>> Wellcome Trust Genome Campus,
>>> Hinxton
>>> Cambridge CB10 1SD,
>>> UK.
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>
> Rhoda Kinsella Ph.D.
> Ensembl Bioinformatician,
> European Bioinformatics Institute (EMBL-EBI),
> Wellcome Trust Genome Campus,
> Hinxton
> Cambridge CB10 1SD,
> UK.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>