I want to convert mouse (MGI) gene symbols to entrez gene ids by using BioMart's R interface (http://www.bioconductor.org/packages/release/bioc/html/biomaRt.html).
I every now and then come across a mouse gene symbol for which BioMart does not find an entrez gene id but interestingly I can find an entrez gene id in the NCBI web site.
For example I use the following R code to try to find an entrez gene id for a gene symbol "0610009E02Rik":
ensembl = useDataset("mmusculus_gene_ensembl", mart=ensembl)
geneSymbs = c("0610009E02Rik")
geneSymbsEntrezGenes <- getBM(attributes=c('mgi_symbol', 'entrezgene'), filters='mgi_symbol', values=geneSymbs, mart=ensembl)
Then I can see it did not find an entrez gene id by giving the following R command:
1 0610009E02Rik NA
However I can find an entrez gene id for this gene symbol in the NCBI web site:
So, to me it seems the version of BioMart (biomaRt_2.18.0) I am using is not up-to-date with NCBI.
Is it perhaps so that the BioMart is compiled periodically (e.g once a month, every second month) from NCBI?
If this is the case, should I perhaps just access NCBI directly and forget BioMart if I want to be sure I get most up-to-date conversions?
Or am I perhaps using an out-dated version of BioMart?