[BioC] problem getting biotype in biomaRt

[steffen at stat.Berkeley.EDU]

Indeed that seems to be the problem.

Cheers,
Steffen

> Hi Steffen and Elizabeth,
> I have had a look through the ensembl mart configuration and have
> found an error which may fix the current gene and transcript biotype
> problem.
> The pointer attribute for the structure_biotype is still pointing to
> biotype so I will change this to point to gene_biotype and this should
> solve the issue. I will
> implement this change for release 53 (approximately mid February). My
> apologies for any inconvenience and thank you for reporting this
> problem.
> Regards,
> Rhoda
>
>
> On 13 Jan 2009, at 10:08, Rhoda Kinsella wrote:
>
>> 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.
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> 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.
>