[BioC] problem with biomaRt

Wed Feb 23 15:08:02 CET 2011

Dear Rhoda,

thank you so much: that solved the problem!

best,
Teresa

ps: sorry, I already found your suggestion about changing the host to
"www.ensembl.org" in a previous email, but [shame on me :D] was not
able to find out how to do it!
This time everything was crystal clear, I was able to fix my problem
just repeating the exact same steps from you email. thanks!

2011/2/23 Rhoda Kinsella <rhoda at ebi.ac.uk>:
> 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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>>>
>>
>> _______________________________________________
>> 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.
>
>