Biomart Errors
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@416ff954
Last seen 4 months ago
Canada

I am receiving the following errors when using Biomart - they seem to be persistent so wanted to see if there is something up with the system. I did check the status and website and both seem to indicate the service is fine.

Thanks for the help/insight.

ensembl <- biomaRt::useMart("ensembl", host = "www.ensembl.org", ssl.verifypeer = FALSE)
biomaRt::getBM(attributes = c('ensembl_gene_id', 'external_gene_name', 'description'), 
               filters = c('ensembl_gene_id'), 
               values = geneIds, 
               mart = biomaRt::useDataset("hsapiens_gene_ensembl",    mart = ensembl))

Human gives one error
Mouse/Rat gives a 500 error

04/15 17:39:32.324 (GMT)
human: Error in biomaRt::getBM(attributes = c("ensembl_gene_id", "external_gene_name", : The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1.
Please report this on the support site at http://support.bioconductor.org
mouse: Error in bmRequest(request = request, ssl.verifypeer = ssl.verifypeer, : Internal Server Error (HTTP 500).
rat: Error in bmRequest(request = request, ssl.verifypeer = ssl.verifypeer, : Internal Server Error (HTTP 500).
biomaRt • 175 views
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Entering edit mode
@kevin
Last seen 4 hours ago
Republic of Ireland

Hey,

The following functions for me, after a few attempts trying to create the connection object, ensembl. Note that, often, the Ensembl server(s) are quite loaded, in which case it can take a few attempts to register the connection object.

Also, by not specifying host = "www.ensembl.org", I am permitting that biomaRt chooses the best Ensembl mirror for me.

geneIds <- c('ENSG00000149311', 'ENSG00000012048', 'ENSG00000139618',
  'ENSG00000185515', 'ENSG00000141510')

require(biomaRt)
ensembl <- useMart('ensembl', dataset = 'hsapiens_gene_ensembl')
annot <- getBM(attributes = c('ensembl_gene_id', 'external_gene_name', 'description'), 
  filters = c('ensembl_gene_id'), 
  values = geneIds, 
  mart = ensembl)

annot
  ensembl_gene_id external_gene_name
1 ENSG00000012048              BRCA1
2 ENSG00000139618              BRCA2
3 ENSG00000141510               TP53
4 ENSG00000149311                ATM
5 ENSG00000185515              BRCC3
                                                                   description
1               BRCA1 DNA repair associated [Source:HGNC Symbol;Acc:HGNC:1100]
2               BRCA2 DNA repair associated [Source:HGNC Symbol;Acc:HGNC:1101]
3                        tumor protein p53 [Source:HGNC Symbol;Acc:HGNC:11998]
4                ATM serine/threonine kinase [Source:HGNC Symbol;Acc:HGNC:795]
5 BRCA1/BRCA2-containing complex subunit 3 [Source:HGNC Symbol;Acc:HGNC:24185]

Kevin

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Thanks, I have seen it work on/off for me today. I'll remove the URL for future auto-mirror handling, thanks for pointing that out.

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