biomaRt rnorvegicus_gene_ensembl not available anymore
1
1
Entering edit mode
Benjamin ▴ 20
@7e36dbc0
Last seen 5 weeks ago
Canada

I use the biomaRt package for my genomic research weekly and I noticed after updating to the latest version of biomaRt that when running the following code, there is no longer a dataset listed for the Rat (Rattus norvegicus). I did test "hsapiens_gene_ensembl", and it is working I am currently running R version 4.4.0 and biomaRt version 2.60.1.

library(biomaRt)

ensemblmart113 <- useEnsembl(biomart="ensembl")
rat <- useDataset("rnorvegicus_gene_ensembl", ensemblmart113)
#Error in checkDataset(dataset = dataset, mart = mart) : 
#The given dataset:  rnorvegicus_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets() function.
listDatasets(ensemblmart113) #no rnorvegicus_gene_ensembl anymore

#sessionInfo
sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS 15.0.1

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Toronto
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] biomaRt_2.60.1

loaded via a namespace (and not attached):
 [1] bit_4.5.0               jsonlite_1.8.9          dplyr_1.1.4             compiler_4.4.0          crayon_1.5.3            filelock_1.0.3          tidyselect_1.2.1       
 [8] Biobase_2.64.0          xml2_1.3.6              blob_1.2.4              stringr_1.5.1           Biostrings_2.72.1       IRanges_2.38.1          progress_1.2.3         
[15] png_0.1-8               fastmap_1.2.0           R6_2.5.1                XVector_0.44.0          generics_0.1.3          curl_5.2.3              httr2_1.0.5            
[22] GenomeInfoDb_1.40.1     BiocGenerics_0.50.0     tibble_3.2.1            AnnotationDbi_1.66.0    GenomeInfoDbData_1.2.12 DBI_1.2.3               pillar_1.9.0           
[29] rlang_1.1.4             utf8_1.2.4              KEGGREST_1.44.1         cachem_1.1.0            stringi_1.8.4           bit64_4.5.2             RSQLite_2.3.7          
[36] memoise_2.0.1           cli_3.6.3               magrittr_2.0.3          zlibbioc_1.50.0         digest_0.6.37           dbplyr_2.5.0            rappdirs_0.3.3         
[43] hms_1.1.3               BiocFileCache_2.12.0    lifecycle_1.0.4         S4Vectors_0.42.1        prettyunits_1.2.0       vctrs_0.6.5             glue_1.8.0             
[50] stats4_4.4.0            fansi_1.0.6             httr_1.4.7              tools_4.4.0             pkgconfig_2.0.3         UCSC.utils_1.0.0

Is there an alternative method for acquiring the rat gene ensemble? Or has this been removed permanently?

If you need any further information from me, I would be happy to provide it.

Rattus_norvegicus biomaRt • 1.3k views
ADD COMMENT
1
Entering edit mode
@james-w-macdonald-5106
Last seen 7 hours ago
United States

The biomaRt package only queries what exists on Ensembl's Biomart database, and if you go directly to their page it's not there. So you should ask Ensembl, since it's their database, rather than asking here, as nobody here (except Mike Smith, who may have to ask Ensembl himself) is likely to have any inside information about what's going on at Ensembl.

0
Entering edit mode

I appreciate the quick reply. I will leave this issue on here (hopefully Mike Smith) will see it. In the mean time, I will look into asking Ensembl directly.

ADD REPLY
1
Entering edit mode

You are not the only biomaRt user to encounter this, and I contacted the Ensembl helpdesk. I got the reply below, which hopefully means it will be resolved soon:

Thank you for contacting the Ensembl helpdesk.

The production team is actively working on bringing back the missing species in BioMart. We are very sorry for any inconvenience this may have caused.

ADD REPLY
1
Entering edit mode

Thanks Mike, I will post here again when this issue gets resolved.

ADD REPLY
0
Entering edit mode

Any update on the resolution to this? I'm having the same issue with another species.

ADD REPLY
0
Entering edit mode

Unfortunately I received this update from the Ensembl Helpdesk on 2024-11-14:

Unfortunately, the fix is taking longer than expected and we apologise for the inconvenience this has caused.

I would suggest you to use the previous version of Ensembl (112) (https://may2024.archive.ensembl.org/biomart/martview/) to work with the missing species.

Not ideal, but they do seem to be working on it.

ADD REPLY

Login before adding your answer.

Traffic: 410 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6