Problem obtaining NCBI gene IDs from Ensembl version 107
2
1
Entering edit mode
@jamiegearing-12556
Last seen 11 months ago
Australia

Hello,

I have just encountered an issue trying to get NCBI gene IDs (entrezgene_id) from Ensembl version 107 using biomaRt. It looks like there could be something missing from the version 107 archive related to these IDs: ensembl_mart_107.hsapiens_gene_ensembl__ox_entrezgene__dm.

I did not encounter a problem just looking at gene names in version 107 or when getting NCBI gene IDs from the new version 108.

Best regards,

Jamie.

library(biomaRt)

mart <- useEnsembl("ensembl", dataset = "hsapiens_gene_ensembl",  version = 107)
query <- c("ENSG00000075624", "ENSG00000111640", "ENSG00000165704")
biomaRt.annotation <- getBM(attributes = c("ensembl_gene_id", "external_gene_name"),
                              filters = "ensembl_gene_id", values = query, mart = mart)
biomaRt.annotation
#  ensembl_gene_id external_gene_name
# 1 ENSG00000075624               ACTB
# 2 ENSG00000111640              GAPDH
# 3 ENSG00000165704              HPRT1                              

biomaRt.annotation <- getBM(attributes = c("ensembl_gene_id", "external_gene_name", "entrezgene_id"),
                               filters = "ensembl_gene_id", values = query, mart = mart)
# Error in .processResults(postRes, mart = mart, hostURLsep = sep, fullXmlQuery = fullXmlQuery,  : 
#  Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'ensembl_mart_107.hsapiens_gene_ensembl__ox_entrezgene__dm' doesn't exist


mart <- useEnsembl("ensembl", dataset = "hsapiens_gene_ensembl")
biomaRt.annotation <- getBM(attributes = c("ensembl_gene_id", "external_gene_name", "entrezgene_id"),
                               filters = "ensembl_gene_id", values = query, mart = mart)
biomaRt.annotation 
#   ensembl_gene_id external_gene_name entrezgene_id
# 1 ENSG00000075624               ACTB            60
# 2 ENSG00000111640              GAPDH          2597
# 3 ENSG00000165704              HPRT1          3251

sessionInfo()
# R version 4.1.2 (2021-11-01)
# Platform: x86_64-apple-darwin17.0 (64-bit)
# Running under: macOS Catalina 10.15.7
# 
# Matrix products: default
# BLAS:   /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
# LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
# 
# locale:
# [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
# 
# attached base packages:
# [1] stats     graphics  grDevices utils     datasets  methods   base     
# 
# other attached packages:
# [1] biomaRt_2.50.1
# 
# loaded via a namespace (and not attached):
# [1] KEGGREST_1.34.0        progress_1.2.2         tidyselect_1.1.1       purrr_0.3.4           
# [5] vctrs_0.3.8            generics_0.1.1         stats4_4.1.2           BiocFileCache_2.2.0   
# [9] utf8_1.2.2             blob_1.2.2             XML_3.99-0.8           rlang_0.4.12          
# [13] pillar_1.6.4           glue_1.6.0             withr_2.4.3            DBI_1.1.1             
# [17] rappdirs_0.3.3         BiocGenerics_0.40.0    bit64_4.0.5            dbplyr_2.1.1          
# [21] GenomeInfoDbData_1.2.7 lifecycle_1.0.1        stringr_1.4.0          zlibbioc_1.40.0       
# [25] Biostrings_2.62.0      memoise_2.0.1          Biobase_2.54.0         IRanges_2.28.0        
# [29] fastmap_1.1.0          GenomeInfoDb_1.30.0    curl_4.3.2             AnnotationDbi_1.56.2  
# [33] fansi_0.5.0            Rcpp_1.0.7             filelock_1.0.2         cachem_1.0.6          
# [37] S4Vectors_0.32.3       XVector_0.34.0         bit_4.0.4              hms_1.1.1             
# [41] png_0.1-7              digest_0.6.29          stringi_1.7.6          dplyr_1.0.7           
# [45] tools_4.1.2            bitops_1.0-7           magrittr_2.0.1         RCurl_1.98-1.5        
# [49] RSQLite_2.2.9          tibble_3.1.6           crayon_1.4.2           pkgconfig_2.0.3       
# [53] ellipsis_0.3.2         xml2_1.3.3             prettyunits_1.1.1      assertthat_0.2.1      
# [57] httr_1.4.2             R6_2.5.1               compiler_4.1.2
biomaRt ensembldb ensembl • 1.3k views
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1
Entering edit mode
@jamiegearing-12556
Last seen 11 months ago
Australia

The underlying BioMart issue has now been fixed by the Ensembl Helpdesk.

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3
Entering edit mode
@james-w-macdonald-5106
Last seen 11 hours ago
United States

You get the same error if you try that query directly on the archive site Biomart server, so it's on their end, not an issue with biomaRt.

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0
Entering edit mode

Thanks James. The same problem does indeed occur accessing the NCBI gene ID table using BioMart from the 107 archive website. However, currently the relevant table is actually accessible via FTP.

I have contacted the Ensembl help desk directly.

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