[BioC] Biomart server down?
Rhoda Kinsella
rhoda at ebi.ac.uk
Fri May 20 17:50:46 CEST 2011
Hi Fabrice
Yes this should be possible if you select a particular regulatory
feature (e.g. feature type -> Gene Associated). I would suggest that
you take a look at the web interface at http://www.ensembl.org/biomart/martview/
and try to construct a query by selecting filters such as region
filter and one or more filter from the regulatory feature filter
section (i.e. feature type or cell type) and then go to the attributes
section and select the attributes you require from the corresponding
regulatory feature attribute page. You can then take a look at the xml
for that query by clicking the xml button and use the internal names
in the construction of your query using the biomaRt package.
Regards
Rhoda
On 20 May 2011, at 16:35, Fabrice Tourre wrote:
> 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]]
>>>>>
>>>>> _______________________________________________
>>>>> 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
>>>>
>>
>> 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.
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