Is it possible to obtain gene description (from gene ids) for D. melanogaster with the biomaRt R package?

Question

[antonioggsousa]

Hi,

I'm interested in to obtain the external gene names and the respective description based on gene ids for the fruit fly (D. melanogaster) model. I thought that biomaRt R package would be a good solution. Therefore I tried the following:

## Convert Geneid into GeneName
#
ensembl <- biomaRt::useMart(biomart = "ensembl", 
                            dataset = "dmelanogaster_gene_ensembl") # select ref db: Drosophila melanogaster genes (BDGP6.28) BDGP6.28
geneName <- biomaRt::getBM( attributes = c("ensembl_gene_id", "external_gene_name", "description"), 
                            filters = "ensembl_gene_id", 
                            values = data$Geneid, 
                            mart = ensembl )

Where the input list is (data$Geneid %>% head):

[1] "FBgn0031081" "FBgn0052826" "FBgn0031085" "FBgn0062565" "FBgn0031088" "FBgn0041626"

And the result is (head(geneName)):

      ensembl_gene_id external_gene_name description
1     FBgn0000022                 ac          NA
2     FBgn0000045             Act79B          NA
3     FBgn0000061                 al          NA
4     FBgn0000092             CG2650          NA
5     FBgn0000100              RpLP0          NA
6     FBgn0000108               Appl          NA

The external gene name is retrieved, but not the description.

Anyone knows if it is possible to get the description from D. melanogaster ensembl gene ids with the biomaRt R package?

If not, can you recommend a R package tool or any other programmatic tool (rather than go to the site and submit a huge list of genes)?

Thanks in advance,

António

Answer 1

[GenoMax]

Using Entrezdirect:

$ more test
FBgn0000022
FBgn0000045
FBgn0000061

$ for i in `cat ./test`; do printf ${i}"\t"; esearch -db gene -query ${i} | esummary | xtract -pattern DocumentSummary -element NomenclatureSymbol,NomenclatureName; done
FBgn0000022 ac  achaete
FBgn0000045 Act79B  Actin 79B
FBgn0000061 al  aristaless

[antonioggsousa]

Thank you!

It works wonderfully!

António