I have an ENSEMBL-based RNA-seq dataset that I would like to annotate. For that I use the library EnsDb.Mmusculus.v79. However, I am somehow not able to retrieve the gene name (description). Based on the retrievable annotation info, I assumed this would be accessible through the argument columns = "GENENAME", but this turns out not to be the case (that rather is the same as "SYMBOL"). See example code below. Am I missing something obvious? Any advise on how to do this would be appreciated.

> library(EnsDb.Mmusculus.v79)
>
> keys <- keys(EnsDb.Mmusculus.v79)[1:15]
> anno.result <- select(EnsDb.Mmusculus.v79, keys=keys, columns=c("GENEID","SYMBOL","GENENAME","ENTREZID"),keytype="GENEID")
>
> anno.result
               GENEID SYMBOL GENENAME ENTREZID
1  ENSMUSG00000000001  Gnai3    Gnai3    14679
2  ENSMUSG00000000003   Pbsn     Pbsn    54192
3  ENSMUSG00000000028  Cdc45    Cdc45    12544
4  ENSMUSG00000000031    H19      H19         
5  ENSMUSG00000000037  Scml2    Scml2   107815
6  ENSMUSG00000000049   Apoh     Apoh    11818
7  ENSMUSG00000000056   Narf     Narf    67608
8  ENSMUSG00000000058   Cav2     Cav2    12390
9  ENSMUSG00000000078   Klf6     Klf6    23849
10 ENSMUSG00000000085  Scmh1    Scmh1         
11 ENSMUSG00000000088  Cox5a    Cox5a    12858
12 ENSMUSG00000000093   Tbx2     Tbx2    21385
13 ENSMUSG00000000094   Tbx4     Tbx4    21387
14 ENSMUSG00000000103   Zfy2     Zfy2         
15 ENSMUSG00000000120   Ngfr     Ngfr    18053
>

For the first gene Gnai3 (ENSMUSG00000000001), description should be "guanine nucleotide binding protein (G protein), alpha inhibiting 3" (according to ENSEMBL website here).

> columns(EnsDb.Mmusculus.v79)
 [1] "ENTREZID"            "EXONID"              "EXONIDX"            
 [4] "EXONSEQEND"          "EXONSEQSTART"        "GENEBIOTYPE"        
 [7] "GENEID"              "GENENAME"            "GENESEQEND"         
[10] "GENESEQSTART"        "INTERPROACCESSION"   "ISCIRCULAR"         
[13] "PROTDOMEND"          "PROTDOMSTART"        "PROTEINDOMAINID"    
[16] "PROTEINDOMAINSOURCE" "PROTEINID"           "PROTEINSEQUENCE"    
[19] "SEQCOORDSYSTEM"      "SEQLENGTH"           "SEQNAME"            
[22] "SEQSTRAND"           "SYMBOL"              "TXBIOTYPE"          
[25] "TXCDSSEQEND"         "TXCDSSEQSTART"       "TXID"               
[28] "TXNAME"              "TXSEQEND"            "TXSEQSTART"         
[31] "UNIPROTDB"           "UNIPROTID"           "UNIPROTMAPPINGTYPE"
>

> sessionInfo()
R version 3.4.0 Patched (2017-05-10 r72670)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base     

other attached packages:
 [1] EnsDb.Mmusculus.v79_2.1.0 ensembldb_2.0.4          
 [3] AnnotationFilter_1.0.0    GenomicFeatures_1.28.4   
 [5] AnnotationDbi_1.38.2      Biobase_2.36.2           
 [7] GenomicRanges_1.28.4      GenomeInfoDb_1.12.2      
 [9] IRanges_2.10.2            S4Vectors_0.14.3         
[11] BiocGenerics_0.22.0      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12                  BiocInstaller_1.26.0         
 [3] AnnotationHub_2.8.2           compiler_3.4.0               
 [5] XVector_0.16.0                ProtGenerics_1.8.0           
 [7] bitops_1.0-6                  tools_3.4.0                  
 [9] zlibbioc_1.22.0               biomaRt_2.32.1               
[11] digest_0.6.12                 bit_1.1-12                   
[13] RSQLite_2.0                   memoise_1.1.0                
[15] tibble_1.3.3                  lattice_0.20-35              
[17] pkgconfig_2.0.1               rlang_0.1.2                  
[19] Matrix_1.2-10                 shiny_1.0.3                  
[21] DelayedArray_0.2.7            DBI_0.7                      
[23] curl_2.8.1                    yaml_2.1.14                  
[25] GenomeInfoDbData_0.99.0       httr_1.2.1                   
[27] rtracklayer_1.36.4            Biostrings_2.44.2            
[29] bit64_0.9-7                   grid_3.4.0                   
[31] R6_2.2.2                      XML_3.98-1.9                 
[33] BiocParallel_1.10.1           blob_1.1.0                   
[35] htmltools_0.3.6               Rsamtools_1.28.0             
[37] matrixStats_0.52.2            GenomicAlignments_1.12.1     
[39] SummarizedExperiment_1.6.3    xtable_1.8-2                 
[41] mime_0.5                      interactiveDisplayBase_1.14.0
[43] httpuv_1.3.5                  RCurl_1.95-4.8               
[45] lazyeval_0.2.0               
>

Dear Guido,

the naming of the columns in an EnsDb might be misleading, but they reflect the naming convention from Ensembl. Each gene there has a name which is stored in columns gene_name (or GENENAME) in the EnsDb. In addition there is the description field for each gene, but I didn't put them in the EnsDb prior to version 2.1 of these databases. In more recent EnsDb databases there is now also a column DESCRIPTION that you can query. You can get such databases from AnnotationHub:

> library(AnnotationHub)
> query(ah, "EnsDb.Mmusculus")
AnnotationHub with 3 records
# snapshotDate(): 2017-07-11
# $dataprovider: Ensembl
# $species: Mus Musculus
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH53222"]]'

            title                            
  AH53222 | Ensembl 87 EnsDb for Mus Musculus
  AH53726 | Ensembl 88 EnsDb for Mus Musculus
  AH56691 | Ensembl 89 EnsDb for Mus Musculus

> edb <- ah[["AH53222"]]
loading from cache '/Users/jo//.AnnotationHub/59960'
> columns(edb)
 [1] "DESCRIPTION"         "ENTREZID"            "EXONID"             
 [4] "EXONIDX"             "EXONSEQEND"          "EXONSEQSTART"       
 [7] "GENEBIOTYPE"         "GENEID"              "GENENAME"           
[10] "GENESEQEND"          "GENESEQSTART"        "INTERPROACCESSION"  
[13] "ISCIRCULAR"          "PROTDOMEND"          "PROTDOMSTART"       
[16] "PROTEINDOMAINID"     "PROTEINDOMAINSOURCE" "PROTEINID"          
[19] "PROTEINSEQUENCE"     "SEQCOORDSYSTEM"      "SEQLENGTH"          
[22] "SEQNAME"             "SEQSTRAND"           "SYMBOL"             
[25] "TXBIOTYPE"           "TXCDSSEQEND"         "TXCDSSEQSTART"      
[28] "TXID"                "TXNAME"              "TXSEQEND"           
[31] "TXSEQSTART"          "TXSUPPORTLEVEL"      "UNIPROTDB"          
[34] "UNIPROTID"           "UNIPROTMAPPINGTYPE"
> genes(edb, filter = ~ gene_id == "ENSMUSG00000000001", columns = c("description", "gene_name"), return.type = "data.frame")
                                                                                           description
1 guanine nucleotide binding protein (G protein), alpha inhibiting 3 [Source:MGI Symbol;Acc:MGI:95773]
  gene_name            gene_id
1     Gnai3 ENSMUSG00000000001

In general I suggest users to fetch EnsDb databases from AnnotationHub. Through AnnotationHub I provide EnsDbs for all species from Ensemb and I'll also add EnsDb databases for each new Ensembl release.

cheers, jo

To my knowledge you aren't missing anything obvious - the gene names aren't part of the EnsDb. You can use biomaRt to get them.