Is The Biomart Registry Accessed Via The Bioconductor Package Out Of Date?

Question

[Georg Summer]

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So the question is: Am I missing something or is the biomaRt package/registry simply out of date?

Answer 1

[Neilfws]

Yes, everything that you state is correct and it seems that version 69 is still the Bioconductor/biomaRt default.

You can use release 71 as explained in this post from the BioC mailing list: Useful information about Ensembl release 71 mart databases.

mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL",
                host = "www.ensembl.org",
                path = "/biomart/martservice",
                dataset = "rnorvegicus_gene_ensembl")

transcript_mart <- getBM(attributes = c("ensembl_transcript_id", "ensembl_gene_id"), 
                         filters = "ensembl_gene_id", 
                         values = "ENSRNOG00000047860", mart = mart)

transcript_mart
 #  ensembl_transcript_id    ensembl_gene_id
 # 1   ENSRNOT00000073930 ENSRNOG00000047860

[Georg Summer]

Thanks for keeping my sanity intact :)