Ensembl Biomart Plant database

Question

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I want to fetch Arabidospsis annotation via ensembl biomart R package, here is the example how I am trying to fetch it:

 library("biomaRt")

 species = athaliana
 db = useMart(biomart = "plants_mart",paste(species,"_eg_gene",sep=""), host = "plants.ensembl.org")

 features = getBM(attributes = c("ensembl_gene_id","external_gene_id","description","entrezgene","chromosome_name","start_position", "end_position"), filters = c("ensembl_gene_id"),values = rownames(dds), mart = ensembl)

>features
[1] ensembl_gene_id external_gene_id description entrezgene chromosome_name start_position end_position <0 rows> (or 0-length row.names)

its showing no entries, can anyone tell me why this is happening?

P.S.I tried with Oryza sativa as well, same issue with that as well

[GenoMax]

Recently similar questions have determined that there was some sort of temporary "timeout" issue. You may want to retry after some time/tomorrow.

Answer 1

[Emily]

Please can you send us a bug report to helpdesk [at] ensemblgenomes.org.

Answer 2

[Mike Smith]

Your example can't be run directly since you haven't provided the dds object that you're using to provide the gene IDs you're interested in. If I run it using three Ensembl IDs as an example, I still get the same result as you. However, if I remove the 'entrezgene' attribute it seems to work e.g.

library("biomaRt")

ensembl <- useMart(biomart = "plants_mart",
                   dataset = "athaliana_eg_gene",
                   host = "plants.ensembl.org")

features <- getBM(attributes = c("ensembl_gene_id",
                                 "external_gene_id",
                                 "description",
                                 "chromosome_name",
                                 "start_position", 
                                 "end_position"), 
                 filters = c("ensembl_gene_id"),
                 values = c('AT1G02170', 
                            'AT1G02180', 
                            'AT1G02190'), 
                 mart = ensembl)

Here's the output:

> features
  ensembl_gene_id external_gene_id                                                  description chromosome_name start_position end_position
1       AT1G02170             AMC1       Metacaspase-1 [Source:UniProtKB/Swiss-Prot;Acc:Q7XJE6]               1         411664       413554
2       AT1G02180                                                                                             1         413522       414649
3       AT1G02190                  Protein CER1-like 1 [Source:UniProtKB/Swiss-Prot;Acc:F4HVX7]               1         415074       418027

I'm afraid I don't really have an answer for why this happens at the moment.

[Mike Smith]

Having thought about this a little more, I wonder if this is the same kind of behaviour noted in this thread on the Bioconductor support forum (https://support.bioconductor.org/p/90966/#91060)

In that example if you asked for both SNPs and phenotype data, valid SNPs were silently dropped if they didn't also contain any phenotype information. You have a different context here, but perhaps if there aren't any entrezgene IDs in the database for you genes we experience a similar phenomena and the results are dropped.