I used the AnnotationDbi::mapIds function over the EnsDb.Mmusculus.v79 package to map Ensembl Gene IDs back to entrez id over a a long vector of ENSG Ids.

I expected this to return a 1:1 mapping when mapIds(..., multiVals='first'), but was surprised that this returned several entrez ids concatenated with ";" for a given ensembl gene id, for instance:

R> mapIds(EnsDb.Mmusculus.v79, 'ENSMUSG00000079658', 'ENTREZID', 'GENEID')
ENSMUSG00000079658 
 "67923;102642819" 

I've long been working under the assumption that the multiVals parameter is meant to control this, and it should only return a single identifier when the appropriate value for that parameter is passed (like 'first', 'last', or 'asNA', even)

I must say, this finding has shaken the bedrock of all things I thought to be true and I'm having a deja vu moment back to 1999 where I'm asking myself again if I actually might be living inside of The Matrix.

Can I get an assist? Thanks :-)

I'm running on the latest bioc, but just to orient ourselves a bit, here some versions of the relevant packages:

EnsDb.Mmusculus.v79_2.1.0
ensembldb_2.0.1
AnnotationDbi_1.38.0

It's in the database that way:

> con <- dbConnect(SQLite(), paste0(path.package("EnsDb.Mmusculus.v79"), "/extdata/EnsDb.Mmusculus.v79.sqlite"))
> dbGetQuery(con, "select * from gene where gene_id='ENSMUSG00000079658';")
             gene_id gene_name        entrezid   gene_biotype gene_seq_start
1 ENSMUSG00000079658     Tceb1 67923;102642819 protein_coding       16641725
  gene_seq_end seq_name seq_strand seq_coord_system
1     16657042        1         -1       chromosome

Which I would imagine reflects a disagreement between EBI and NCBI as to what is and is not Tceb1.

Hi Steve,

I've fixed the issue with the concatenated Entrezgene IDs. What you need is an ensembldb version >= 2.0.2 (in Bioc 3.5, or the newest Bioc devel version) and an updated EnsDb database/package. Might take some days until the updated EnsDb packages are online (most likely only available in BioC 3.6-devel though), but you can fetch the new EnsDbs already from AnnotationHub (for Ensembl releases 87 and 88):

> library(AnnotationHub)
> ah <- AnnotationHub()
snapshotDate(): 2017-04-25
## Get the (updated) EnsDb for Mus Musculus and Ensembl version 87
> edb <- query(ah, c("EnsDb", "Mus Musculus", "87"))[[1]]
require(“ensembldb”)
downloading from 'https://annotationhub.bioconductor.org/fetch/59960'
retrieving 1 resource
  |======================================================================| 100%
## Check DBSCHEMAVERSION, it should be 2.0 for it to work
> edb
EnsDb for Ensembl:
|Backend: SQLite
|Db type: EnsDb
|Type of Gene ID: Ensembl Gene ID
|Supporting package: ensembldb
|Db created by: ensembldb package from Bioconductor
|script_version: 0.3.0
|Creation time: Sun May 21 00:52:00 2017
|ensembl_version: 87
|ensembl_host: localhost
|Organism: mus_musculus
|taxonomy_id: 10090
|genome_build: GRCm38
|DBSCHEMAVERSION: 2.0
| No. of genes: 50143.
| No. of transcripts: 124168.
|Protein data available.
> mapIds(edb, 'ENSMUSG00000079658', 'ENTREZID', 'GENEID')
ENSMUSG00000079658
             67923

Interestingly, in Ensembl 87 this gene is annotated to only a signle Entrezgene.

> mapIds(edb, 'ENSMUSG00000079658', 'ENTREZID', 'GENEID', multiVals = "list")
$ENSMUSG00000079658
[1] 67923

But it works for others with multimappings:

> mapIds(edb, 'ENSMUSG00000091318', 'ENTREZID', 'GENEID', multiVals = "list")
$ENSMUSG00000091318
[1] 408191 408192

Hope this simplifies your workflow.

cheers, jo