Connect to the appropriate Biomart database

Question

Biomart and ensembl not working?

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Zuzer • 0

@7b338335

Last seen 6 hours ago

United States

data<- res_tbl

Connect to the appropriate Biomart database

ensembl <- useEnsembl(biomart = "ensembl", dataset = "mmusculus_gene_ensembl", version = 102)

Error in bmRequest(request = request, httr_config = httr_config, verbose = verbose) : Not Found (HTTP 404)

also tried to work around

ensembl <- useEnsembl(biomart = "ensembl", dataset = "mmusculus_gene_ensembl", mirror = "useast")

Define Ensembl IDs from your data

ensembl_ids <- data$ENSEMBL

Retrieve gene annotations for the Ensembl IDs

gene_annotations <- getBM(attributes = c("ensembl_gene_id", "external_gene_name"),

filters = "ensembl_gene_id",

values = ensembl_ids,

mart = ensembl) Batch submitting query [========>-------------------------------------------] 17% eta: 15sError: biomaRt has encountered an unknown server error. HTTP error code: 504 Please report this on the Bioconductor support site at https://support.bioconductor.org/ Consider trying one of the Ensembl mirrors (for more details look at ?useEnsembl)

ensembldb biomaRt • 78 views

ADD COMMENT • link updated 2 hours ago by James W. MacDonald 67k • written 14 hours ago by Zuzer • 0

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I have the same problem for the last ~30h

 ensembl <- biomaRt::useEnsembl(biomart = "ensembl", dataset = "mmusculus_gene_ensembl", mirror = "useast")

Output:

Ensembl site unresponsive, trying www mirror
Ensembl site unresponsive, trying asia mirror
Error in .chooseEnsemblMirror(mirror = mirror, http_config = http_config) : 
  Unable to query any Ensembl site

ADD REPLY • link 6 hours ago Irene • 0

score 0 · Answer 1 · 2025-01-15

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 1 hour ago

United States

Unfortunately the Ensembl websites can be a bit unstable. The only recourse that I know of is patience and trying later. It appears to be currently available (useast at least), so you might try again

ADD COMMENT • link 2 hours ago James W. MacDonald 67k

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It seems to be working for mouse but not for human

ensembl <- biomaRt::useEnsembl(biomart = "ensembl", dataset = "hsapiens_gene_ensembl", mirror = "useast")
Ensembl site unresponsive, trying asia mirror
Ensembl site unresponsive, trying www mirror
Error in .chooseEnsemblMirror(mirror = mirror, http_config = http_config) : 
  Unable to query any Ensembl site
> ensembl <- biomaRt::useEnsembl(biomart = "ensembl", dataset = "mmusculus_gene_ensembl", mirror = "useast")
>

ADD REPLY • link 2 hours ago Irene • 0

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> library(biomaRt)
> mart <- useEnsembl("ensembl","hsapiens_gene_ensembl")
Ensembl site unresponsive, trying useast mirror
> mart
Object of class 'Mart':
  Using the ENSEMBL_MART_ENSEMBL BioMart database
  Using the hsapiens_gene_ensembl dataset>

ADD REPLY • link 2 hours ago James W. MacDonald 67k