[BioC] biomaRt - attribute mirbase is missing

[Neel Aluru]

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