Query ERROR

[Struggle-Lee]

when i use biomaRt to transfer IDs, this error emerged recent days, could you please help me
getBM(filters = 'uniprotswissprot', attributes = c("hgnc_symbol"), values="P02768", mart=useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl"))

the error information is :Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery, :
Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'ensembl_mart_112.hsapiens_gene_ensembl__ox_hgnc__dm' doesn't exist

I have tried the example code, and the same error was reported, maybe it's my internet problem?

[duoangelo]

I'm experiencing the same issue with the biomaRt package when trying to retrieve gene information.
biomaRt::getBM(
mart = mart,
useCache = FALSE,
values = "FANCL",
filters = "hgnc_symbol",
attributes = c(
"ensembl_gene_id", "external_gene_source",
"gene_biotype"
)
)

I receive this error message:

Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery, :
Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'ensembl_mart_112.hsapiens_gene_ensembl__ox_hgnc__dm' doesn't exist

[hxjsxd]

I am having the same issue for the past hours and I was hoping to find a solution
The same error also shows up with VISEAGO package when I try to load GO annotations from Ensembl

[Natafui]

I am also having the same issue this morning, and this is exact (word-for-word) code that I've used before in the past with no issues. I think it's something on their end, although not sure on specifics.

[grimbough]

Unfortunately this is an issue with the Ensembl BioMart server, rather than something I can tackle in the biomaRt package. You get the same error if you use the web interface at https://www.ensembl.org/biomart/martview/ e.g.

Ensembl 112 was release yesterday (https://www.ensembl.info/2024/05/13/ensembl-112-has-been-released/), so hopefully this is a transitory issue releated to that which will be resolved in a few hours/days.

If not then I suggest raising the issue with Ensembl directly via their helpdesk (https://www.ensembl.org/Help/Contact).

[duoangelo]

Thank you for the clarification and prompt response @grimbough . I will reach out to the Ensembl helpdesk if the issue persists.

[vhaghani26]

As others have mentioned, I am rerunning code that I have run verbatim to regenerate a figure, and I was met with this error. Hopefully it is resolved soon!

[grimbough]

I should have also pointed out that you can use the version argument to useEnsembl() to select an older version of Ensembl, where hopefully the error you're all encountering isn't present. For example this currently fails:

library(biomaRt)

ensembl_112 <- useEnsembl(biomart = "genes",
                          dataset = "hsapiens_gene_ensembl")

getBM(filters = 'uniprotswissprot', 
      attributes = c('hgnc_symbol', 'uniprotswissprot'), 
      values = "P02768", 
      mart = ensembl_112)
#> Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery, : 
# Query ERROR: caught BioMart::Exception::Database: Error during query execution: 
# Table 'ensembl_mart_112.hsapiens_gene_ensembl__ox_hgnc__dm' doesn't exist

but you can use the Ensembl 110 archive to get results that were in the database from July 2023. In many cases this will be sufficient to continue working on an analysis.

ensembl_110 <- useEnsembl(biomart = "genes",
                          dataset = "hsapiens_gene_ensembl",
                          version = 110)

getBM(filters = 'uniprotswissprot', 
      attributes = c('hgnc_symbol', 'uniprotswissprot'), 
      values = "P02768", 
      mart = ensembl_110)
#>   hgnc_symbol uniprotswissprot
#> 1         ALB           P02768

---

P.S. for some reason the entire 111 archive is unavailable at this time, so 110 is the newest one you can use right now.