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So the question is: Am I missing something or is the biomaRt package/registry simply out of date?
•
written
by
Georg Summer
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
Thanks for keeping my sanity intact :)
•
written
by
Georg Summer
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