[BioC] problem with biomaRt
Rhoda Kinsella
rhoda at ebi.ac.uk
Wed Feb 23 14:21:24 CET 2011
Hi Teresa
Please try connecting to the Ensembl marts at Ensembl by using host="www.ensembl.org
". I have included my sessionInfo (I use an older version), but please
try my commands and see if you get the results you need:
> sessionInfo()
R version 2.9.2 (2009-08-24)
i386-apple-darwin8.11.1
locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
> library(biomaRt)
> ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
> dataset="hsapiens_gene_ensembl"
> ensembl=useDataset(dataset, mart=ensembl)
Checking attributes ... ok
Checking filters ... ok
> getBM("ensembl_gene_id", "hgnc_symbol", "FUS", ensembl)
ensembl_gene_id
1 ENSG00000089280
>
I hope this helps
Regards
Rhoda
On 23 Feb 2011, at 12:13, Teresa Colombo wrote:
> Hi,
>
> I am also having troubles with biomaRt since last Monday. I've been
> following threads on the topic in the Bioconductor mailing list these
> days trying to find a solution, but could not solve it yet.
> Following Jim suggestion's, today I tried updating R from version 2.11
> to 2.12 and so the biomaRt package from 2.4 to 2.6, but this
> unfortunately did not solve the problem.
>
> Any further suggestion?
>
> thank you in advance,
>
> Teresa
>
> ____________________________
> Teresa Colombo, PhD
> Dept of Cellular Biotechnology and Hematology
> 'Sapienza' University of Rome
> Phone/Fax: +39 06 4457731
>
>
>
>> library(biomaRt)
>> mart <- useMart("ensembl","hsapiens_gene_ensembl")
>> getBM("ensembl_gene_id","hgnc_symbol", "FUS", mart)
> Errore in getBM("ensembl_gene_id", "hgnc_symbol", "FUS", mart) :
> Query ERROR: caught BioMart::Exception::Database: Could not connect
> to mysql database ensembl_mart_61: DBI
> connect('database=ensembl_mart_61;host=dcc-qa-
> db.oicr.on.ca;port=3306','bm_web',...)
> failed: Can't connect to MySQL server on 'dcc-qa-db.oicr.on.ca' (113)
> at /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/
> Configuration/DBLocation.pm
> line 98
>> sessionInfo()
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-redhat-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8
> [5] LC_MONETARY=C LC_MESSAGES=it_IT.UTF-8
> [7] LC_PAPER=it_IT.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] biomaRt_2.6.0
>
> loaded via a namespace (and not attached):
> [1] RCurl_1.5-0 XML_3.2-0
>
>
>
>
>
>
>
> 2011/2/22 James W. MacDonald <jmacdon at med.umich.edu>:
>> Hi Stephanie,
>>
>>
>> On 2/21/2011 6:29 PM, Stefanie Carola Gerstberger wrote:
>>>
>>> Hi all,
>>> I frequently use R biomaRt for querying ensembl. Over the weekend I
>>> experienced a problem with biomaRt. whatever I query I get
>>>
>>>> library(biomaRt)
>>>> ensembl=useMart("ensembl")
>>>> listDatasets(ensembl)
>>>> ens_sap=useMart("ensembl", dataset="hsapiens_gene_ensembl")
>>>> attr_sap=listAttributes(ens_sap)
>>>> filter_sap=listFilters(ens_sap)
>>
>> I get
>>
>>> library(biomaRt)
>>> mart <- useMart("ensembl","hsapiens_gene_ensembl")
>>> getBM("ensembl_gene_id","hgnc_symbol", "FUS", mart)
>> ensembl_gene_id
>> 1 ENSG00000089280
>>> sessionInfo()
>> R version 2.12.0 Patched (2010-11-23 r53652)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>> [1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
>> [3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
>> [5] LC_MONETARY=C LC_MESSAGES=en_US.iso885915
>> [7] LC_PAPER=en_US.iso885915 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] biomaRt_2.6.0
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_1.5-0 XML_3.2-0
>>
>>
>> What is the output of sessionInfo() for you?
>>
>> Best,
>>
>> Jim
>>
>>
>>>>
>>>
>>>> getBM(attributes="ensembl_gene_id", filters="hgnc_symbol",
>>>> values="FUS",
>>>> mart=ens_sap)
>>>
>>> Error in getBM(attributes = "ensembl_gene_id", filters =
>>> "hgnc_symbol", :
>>> Query ERROR: caught BioMart::Exception::Database: Could not
>>> connect to
>>> mysql
>>> database ensembl_mart_61: DBI
>>>
>>> connect('database=ensembl_mart_61;host=dcc-qa-
>>> db.oicr.on.ca;port=3306','bm_web',...)
>>> failed: Can't connect to MySQL server on 'dcc-qa-
>>> db.oicr.on.ca' (113) at
>>>
>>> /srv/biomart_server/biomart.org/biomart-perl/lib/BioMart/
>>> Configuration/DBLocation.pm
>>> line 98
>>>
>>>> getBM(attributes="ensembl_gene_id", filters="refseq_dna",
>>>> values="NM_001134363", mart=ens_sap)
>>>
>>>
>>> I asked ensembl help desk and they advised me to use directly
>>> ensembl mart
>>> through this:
>>>
>>>> library(biomaRt)
>>>> ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
>>>> dataset="hsapiens_gene_ensembl"
>>>> ensembl=useDataset(dataset, mart=ensembl)
>>>
>>> ..however when I try this command I get the following:
>>>
>>>> ensembl=useMart("ENSEMBL_MART_ENSEMBL", host="www.ensembl.org")
>>>
>>>
>>> Space required after the Public Identifier
>>> SystemLiteral " or ' expected
>>> SYSTEM or PUBLIC, the URI is missing
>>> Error: 1: Space required after the Public Identifier
>>> 2: SystemLiteral " or ' expected
>>> 3: SYSTEM or PUBLIC, the URI is missing
>>>
>>>
>>> Does anyone know how to fix this problem?
>>>
>>> Thanks a lot,
>>> Stefanie
>>>
>>> _______________________________________________
>>> 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
>>
>> --
>> James W. MacDonald, M.S.
>> Biostatistician
>> Douglas Lab
>> University of Michigan
>> Department of Human Genetics
>> 5912 Buhl
>> 1241 E. Catherine St.
>> Ann Arbor MI 48109-5618
>> 734-615-7826
>> **********************************************************
>> Electronic Mail is not secure, may not be read every day, and
>> should not be
>> used for urgent or sensitive issues
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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.
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