Dear all,

I am attempting to retrieve transcript biotypes for ncRNAs using Bioconductors's biomaRt in GRCh37 as follows:

library(biomaRt)
ensembl <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", dataset="hsapiens_gene_ensembl") 

# biotypes for mRNAs are obtained fine
refseqids_nm = c("NM_152486","NM_080605", "NM_031921")
getBM(attributes=c("refseq_mrna", "transcript_biotype"), filters="refseq_mrna", values=refseqids_nm, mart=ensembl)
#  refseq_mrna transcript_biotype
#1   NM_031921     protein_coding
#2   NM_080605     protein_coding
#3   NM_152486     protein_coding

# However not for ncRNAs
refseqids_nr = c("NR_015434", "NR_036637")
getBM(attributes=c("refseq_ncrna", "transcript_biotype"), filters="refseq_ncrna", values=refseqids_nr, mart=ensembl)
#[1] refseq_ncrna       transcript_biotype
#<0 rows> (or 0-length row.names)

When I try the same as above but with the current release of Ensembl:

ensembl <- useMart(biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl")
getBM(attributes=c("refseq_ncrna", "transcript_biotype"), filters="refseq_ncrna", values=refseqids_nr, mart=ensembl)
#  refseq_ncrna   transcript_biotype
#1    NR_015434            antisense
#2    NR_036637 processed_transcript

Then I get biotypes for ncRNAs just fine.

Perhaps there is something I am missing here. Does GRCh37 have annotations for ncRNAs? If so, any input on how I can obtain transcript biotypes using biomaRt as above?

Thanks, Sergio