[BioC] biomaRt error

[Rhoda Kinsella]

Hi Iain
Yes there seems to have been problems connecting to the  
www.biomart.org registry which have now been resolved by the Biomart  
team at the OICR. As an alternative,  you can also access the Ensembl  
databases from the Ensembl biomart installation at www.ensembl.org  
using the following biomaRt commands:

 > library(biomaRt)
 > listMarts(host = "www.ensembl.org");
biomart version
1 ENSEMBL_MART_ENSEMBL Ensembl 56
2 ENSEMBL_MART_SNP Ensembl variation 56
3 ENSEMBL_MART_FUNCGEN Ensembl functional genomics 56
4 ENSEMBL_MART_VEGA Vega 36
5 REACTOME Reactome
6 wormbase_current WormBase (CSHL US)
7 pride PRIDE (EBI UK)
 > mart = useMart("ENSEMBL_MART_ENSEMBL", host = "www.ensembl.org")
etc...

Regards
Rhoda


On 14 Jan 2010, at 09:37, Iain Gallagher wrote:

> Seems to be ok this morning. Ran the same query with no problems.  
> Perhaps some transient changes at the server end.
>
> Cheers
>
> Iain
>
> --- On Wed, 13/1/10, Paul Leo <p.leo at uq.edu.au> wrote:
>
>> From: Paul Leo <p.leo at uq.edu.au>
>> Subject: Re: [BioC] biomaRt error
>> To: "Iain Gallagher" <iaingallagher at btopenworld.com>
>> Cc: bioconductor at stat.math.ethz.ch
>> Date: Wednesday, 13 January, 2010, 23:45
>> Dito.
>> Actually 3 days ago some of my old queries started
>> returning different
>> numbers of rows
>>
>>
>> length(unique(ann.all[ann.all[,"gene_biotype"]=="protein_coding"
>> ,
>> "ensembl_gene_id"]))
>> [1] 19940
>>
>>>
>> length 
>> (unique 
>> (ann.all.entrez[ann.all.entrez[,"gene_biotype"]=="protein_coding"
>> , "ensembl_gene_id"])) # 22836
>> [1] 22836
>>
>> vs for months before hand and 4 days previous
>>
>> length(unique(ann.all[ann.all[,"gene_biotype"]=="protein_coding"
>> ,
>> "ensembl_gene_id"]))
>> [1] 22836
>>
>>>
>> length 
>> (unique 
>> (ann.all.entrez[ann.all.entrez[,"gene_biotype"]=="protein_coding"
>> , "ensembl_gene_id"])) # 22836
>> [1] 22836
>>
>> FOR
>> a.filter<-c( "chromosome_name", "start" , "end")
>> fil.vals<-list(chrom,  low.cut, high.cut)
>>
>> ann.all<-getBM(attributes =
>> c 
>> ("ensembl_gene_id 
>> ","external_gene_id 
>> ","chromosome_name 
>> ","start_position 
>> ","end_position","strand","gene_biotype","mgi_symbol","description"),
>> filters = a.filter, values=fil.vals, mart = mart)
>>
>> ann.all.entrez<-getBM(attributes =
>> c(
>> "ensembl_gene_id 
>> ","external_gene_id 
>> ","ensembl_transcript_id 
>> ","chromosome_name 
>> ","start_position 
>> ","end_position 
>> ","strand","gene_biotype","entrezgene","mgi_symbol","description"),
>> filters = a.filter, values=fil.vals, mart = mart)
>>
>> No idea why the first query was affected and not the
>> second.... This did
>> coincide with a bioC update I did two days ago... but that
>> may be a
>> coincidence....
>>
>>
>>
>>
>> Today I get the same error
>>> listMarts()
>> Error: non-BioMart die():
>> not well-formed (invalid token) at line 1, column 11797,
>> byte 11797
>> at /usr/lib/perl5/XML/Parser.pm line 187
>>
>>   does not seem to be XML, nor to identify a file
>> name
>>
>>
>>
>>
>>> sessionInfo()
>> R version 2.10.1 (2009-12-14)
>> x86_64-pc-linux-gnu
>>
>> locale:
>> [1] LC_CTYPE=en_AU.UTF-8
>>    LC_NUMERIC=C
>>
>> [3] LC_TIME=en_AU.UTF-8
>> LC_COLLATE=en_AU.UTF-8
>> [5] LC_MONETARY=C
>>   LC_MESSAGES=en_AU.UTF-8
>> [7] LC_PAPER=en_AU.UTF-8
>>    LC_NAME=C
>>
>> [9] LC_ADDRESS=C
>>    LC_TELEPHONE=C
>>
>> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>>
>>
>> attached base packages:
>> [1] stats     graphics  grDevices
>> utils     datasets  methods
>> base
>>
>> other attached packages:
>> [1] org.Mm.eg.db_2.3.6  RSQLite_0.8-1
>>    DBI_0.2-5
>>
>> [4] AnnotationDbi_1.8.1 Biobase_2.6.1
>>    biomaRt_2.2.0
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_1.3-1  tcltk_2.10.1 tools_2.10.1
>> XML_2.6-0
>>
>>
>>
>> -----Original Message-----
>> From: Iain Gallagher <iaingallagher at btopenworld.com>
>> To: bioconductor at stat.math.ethz.ch
>> Subject: [BioC] biomaRt error
>> Date: Wed, 13 Jan 2010 19:00:14 +0000 (GMT)
>>
>> Hello List
>>
>> Can anyone shed any light on the following biomaRt error?
>> Has something changed at Ensembl?
>>
>>> library(biomaRt)
>>>
>>> mart <- useMart("ensembl",
>> dataset="hsapiens_gene_ensembl")
>> Error: non-BioMart die():
>> not well-formed (invalid token) at line 1, column 11797,
>> byte 11797 at /usr/lib/perl5/XML/Parser.pm line 187
>>
>>   does not seem to be XML, nor to identify a file
>> name
>>> sessionInfo()
>> R version 2.10.1 (2009-12-14)
>> x86_64-pc-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=en_GB.UTF-8
>> [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_2.2.0
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_1.3-1 XML_2.6-0
>>>
>>
>> Thanks
>>
>> Iain
>>
>>
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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.