[BioC] biomaRt - attribute mirbase is missing

[Rhoda Kinsella]

Hi Neel
This omission has also been reported by another Ensembl user and we  
will reinstate this attribute in the release 61 marts in January.  
Apologies for any inconvenience caused.
Regards
Rhoda


On 14 Dec 2010, at 23:20, Neel Aluru wrote:

> Hello Bioc users,
>
> I am having trouble in finding attribute "mirbase" in the biomaRt  
> latest ensembl version. I can find it in the ensembl_mart_51 version  
> but not in the latest version (ENSEMBL GENES 60). Is there any way  
> to add that attribute so that the latest miRNA coordinates can be  
> retrieved.
>
> Thank you,
>
> Neel
>
>
> Here is my session info.
>
> R version 2.11.1 (2010-05-31)
> Copyright (C) 2010 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
>
> [R.app GUI 1.34 (5589) i386-apple-darwin9.8.0]
> biomaRt 2.4.0
>
>> library("biomaRt")
>> listMarts()
>                      
> biomart                                                  version
> 1                    ensembl                             ENSEMBL  
> GENES 60 (SANGER UK)
> 2                        snp                        ENSEMBL   
> VARIATION 60 (SANGER UK)
> 3        functional_genomics               ENSEMBL FUNCTIONAL  
> GENOMICS 60 (SANGER UK)
> 4                       vega                                      
> VEGA 40  (SANGER UK)
>
>> listMarts(archive=TRUE)
>                       biomart                     version
> 1              ensembl_mart_51                  Ensembl 51
> 2                  snp_mart_51                      SNP 51
> 3                 vega_mart_51                     Vega 32
> 4              ensembl_mart_50                  Ensembl 50
> 5                  snp_mart_50                      SNP 50
> 6                 vega_mart_50                     Vega 32
> 7              ensembl_mart_49   ENSEMBL GENES 49 (SANGER)
>
>> ensembl=useDataset("drerio_gene_ensembl", mart= ensembl)
> Checking attributes ... ok
> Checking filters ... ok
>
>> filters=listFilters(ensembl)
>> filters
>                                       
> name                                             description
> 24                             
> with_mirbase                                      with miRBase ID(s)
> 25                               
> with_rfamR                                         with Rfam ID(s)
>> attributes = listAttributes(ensembl)
>> attributes
> # I DO NOT FIND mirbase in this list.
>> miRNA =  
>> getBM 
>> (c("mirbase","ensembl_gene_id","start_position","chromosome_name"),  
>> filters=c("chromosome_name","with_mirbase"), values= list(13,  
>> TRUE), mart = ensembl)
> Error in getBM(c("mirbase", "ensembl_gene_id", "start_position",  
> "chromosome_name"),  :
>  Invalid attribute(s): mirbase
>
> # When I change the database to ensembl_mart_51, mirbase appears.
>> ensembl = useMart("ensembl_mart_51", dataset =  
>> "drerio_gene_ensembl",archive=TRUE)
> Checking attributes ... ok
> Checking filters ... ok
>> listAttributes(ensembl)
>                                            
> name                              description
>
> 34                                       
> mirbase                                  miRBase
>
>
>
>
>
>
>
> Neel Aluru
> Postdoctoral Scholar
> Biology Department
> Woods Hole Oceanographic Institution
> Woods Hole, MA 02543
> USA
> 508-289-3607
>
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Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.