[BioC] problem getting biotype in biomaRt

[Rhoda Kinsella]

Hi Steffen and Elizabeth,
The biotype attribute was changed into gene_biotype and  
transcript_biotype after a user requested that
we provide the transcript_biotype information. I have carried out the  
query below on the Ensembl mart web interface and
there are no errors reported. Steffan, can you provide me with some  
more information about where you think
the source of the problem is and I can help look into this?
Kind regards,
Rhoda




On 12 Jan 2009, at 20:48, steffen at stat.berkeley.edu wrote:

> Hi Elizabeth,
>
> The biotype attribute seem to have changed into a separate  
> gene_biotype
> and transcript_biotype  these two represent the same info.
>
> These two new attributes however are indeed currently not  
> retrievable and
> I am investigating what causes this. It looks like it is on the  
> BioMart
> side.
>
> Cheers,
> Steffen
>
>
>
>> Hi,
>> I am trying to pull down information from Ensembl using biomaRt and I
>> can't get the relevant biotype information (for Human). The old
>> 'biotype' attribute doesn't exist, so what I see is 'gene_biotype'  
>> and
>> 'structure_biotype'. I have no idea what the difference is, but I  
>> can't
>> get either one. The error says it's probably an internal error to be
>> reported, but I also get this when I try to bring down what I think  
>> are
>> incompatible attributes.
>> Thanks,
>> Elizabeth
>>
>>> library(biomaRt)
>>> mart<-useMart("ensembl",dataset= "hsapiens_gene_ensembl")
>> Checking attributes and filters ... ok
>>> martAttr<-listAttributes(mart)
>>> att<-c("ensembl_gene_id",
>> +                 "ensembl_transcript_id",
>> +                 "ensembl_exon_id",
>> +                  "exon_chrom_start",
>> +                  "exon_chrom_end",
>> +                  "strand",
>> +                  "chromosome_name",
>> +                  "rank",
>> +                  "3_utr_start","3_utr_end",
>> +                  "5_utr_start","5_utr_end"
>> +                  )
>>> all(att%in%martAttr[,1]) #valid names for the mart
>> [1] TRUE
>> #works fine here
>>> tempGene <-
>> getBM(att,filter="ensembl_gene_id",value="ENSG00000187634",mart =  
>> mart)
>> #error
>>> tempGene <-
>> getBM 
>> (c 
>> (att 
>> ,"gene_biotype 
>> "),filter="ensembl_gene_id",value="ENSG00000187634",mart
>> = mart)
>>
>>                                 V1
>> 1 Query ERROR: caught BioMart::Exception::Usage: Attributes from
>> multiple attribute pages are not allowed
>> Error in getBM(c(att, "gene_biotype"), filter = "ensembl_gene_id",  
>> value
>> = "ENSG00000187634",  :
>>   Number of columns in the query result doesn't equal number of
>> attributes in query.  This is probably an internal error, please  
>> report.
>> #again an error
>>> tempGene <-
>> getBM 
>> (c 
>> (att 
>> ,"structure_biotype 
>> "),filter="ensembl_gene_id",value="ENSG00000187634",mart
>> = mart)
>>
>>    V1
>> 1 Query ERROR: caught BioMart::Exception::Usage: Attribute biotype  
>> NOT
>> FOUND
>> Error in getBM(c(att, "structure_biotype"), filter =  
>> "ensembl_gene_id",  :
>>   Number of columns in the query result doesn't equal number of
>> attributes in query.  This is probably an internal error, please  
>> report.
>>> sessionInfo()
>> R version 2.8.1 (2008-12-22)
>> i386-pc-mingw32
>>
>> locale:
>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>> [1] biomaRt_1.16.0
>>
>> loaded via a namespace (and not attached):
>> [1] RCurl_0.93-0 tools_2.8.1  XML_1.99-0
>>
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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.