external_gene_id attribute removed from new biomaRt version

Question: external_gene_id attribute removed from new biomaRt version

3 months ago by

Didi • 10

Didi • 10 wrote:

Hi,

I couldn't find the externalgeneid attribute in the new biomaRt version.

Is there any reason for that?

Thanks a lot.

biomart ensembl ensemblplants • 117 views

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written 3 months ago by Didi • 10

Which dataset are you trying to use? I'm not sure there has ever been an external_gene_id attribute for hsapiens (at least not looking at archives back for the past few years), do you mean to use external_gene_name?

You can search for the available attributes with searchAttributes() e.g to look in the October 2016 archive you can use

library(biomaRt)
mart <- useEnsembl('ensembl', dataset = 'hsapiens_gene_ensembl', version = "86")
searchAttributes(mart = mart, "external_gene")

ADD REPLY • link written 3 months ago by Mike Smith • 4.0k

Hi,

I'm using :

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"),
                  filters = c("ensembl_gene_id"), 
                  values=c('AT1G01480', 
                           'AT1G01580'), 
                  mart = ensembl)

ADD REPLY • link modified 3 months ago • written 3 months ago by Didi • 10

Ensembl Plants has fewer archives than the main Ensembl site (I only know of http://oct2017-plants.ensembl.org ) so it's harder to check if things have changed, but I don't see an external_gene_id there either:

> ensembl <- useMart(biomart = "plants_mart",
+                    dataset = "athaliana_eg_gene",
+                    host = "http://oct2017-plants.ensembl.org")
> searchAttributes(ensembl, "external")
                    name         description         page
15    external_gene_name           Gene name feature_page
16  external_gene_source Source of gene name feature_page
142   external_gene_name           Gene name    structure
143 external_gene_source Source of gene name    structure
173   external_gene_name           Gene name     homologs
174 external_gene_source Source of gene name     homologs
904   external_gene_name           Gene name          snp
905 external_gene_source Source of gene name          snp
950   external_gene_name           Gene name    sequences
951 external_gene_source Source of gene name    sequences

Of course it could have been introduced and then removed again between then and now.

I should have mentioned in my previous post that this isn't something that the biomaRt package has introduced. It only allows you to access whatever data and options Ensembl make available. If something has changed or been removed then you probably want to contact the Ensembl helpdesk for an explanation (http://ensemblgenomes.org/info/about/contact ).

ADD REPLY • link written 3 months ago by Mike Smith • 4.0k

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