I am in the process of updating some annotations using the Ensembl Biomart. Using the biomaRt package in R I do the following:
mart = useMart("ensembl", dataset="rnorvegicus_gene_ensembl") transcript_mart = getBM( attributes = c( "ensembl_transcript_id", "ensembl_gene_id"), filters="ensembl_gene_id", values="ENSRNOG00000047860", mart=mart)
The result is empty. I check on the website and get a result:
Ensembl Gene ID Ensembl Transcript ID ENSRNOG00000047860 ENSRNOT00000073930
So the thing is: The website uses Ensembl Genes 71 (the example gene was added with the new rat genome assembly in 70). I check the biomaRt package and it is the current 2.16.0.
listMarts() biomart version 1 ensembl ENSEMBL GENES 69 (SANGER UK)
tells me though that biomaRt 69 is current.
listDatasets(mart) dataset description version 12 rnorvegicus_gene_ensembl Rattus norvegicus genes (RGSC3.4) RGSC3.4
And uses the old genome assembly.
If I check the Biomart registry
Still the old version 69 marts are listed.
So the question is: Am I missing something or is the biomaRt package/registry simply out of date?