Ensembl Biomart Plant database

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

r bioconductor biomart

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updated 9.3 years ago by Mike Smith

• written 9.3 years ago by ####

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

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written 9.3 years ago by GenoMax

2 answers

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

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written 9.3 years ago by Emily

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.

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written 9.3 years ago by 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.

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written 9.3 years ago by Mike Smith