Issues with retrieving Zea mays genes dataset: biomaRt error: looks like we're connecting to incompatible version of BioMart.
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0
Entering edit mode
2044291597 • 0
@d88d418c
Last seen 2 days ago
china

Hi, I am having issues with retrieving Zea mays genes dataset, could you please fix it?

library(biomaRt)
host = "https://plants.ensembl.org"
listMarts(host = host)
ensembl <- useEnsembl(biomart = "plants_mart", host = host)
ensembl |> listDatasets()
ensembl <- useDataset(dataset = "zmays_eg_gene", mart = ensembl)

################################
sessionInfo( )
R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8  LC_CTYPE=Chinese (Simplified)_China.utf8    LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
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] rappdirs_0.3.3          utf8_1.2.4              generics_0.1.3          xml2_1.3.6              RSQLite_2.3.7           stringi_1.8.4           hms_1.1.3               digest_0.6.37          
 [9] magrittr_2.0.3          fastmap_1.2.0           blob_1.2.4              jsonlite_1.8.8          progress_1.2.3          AnnotationDbi_1.66.0    GenomeInfoDb_1.40.1     DBI_1.2.3              
[17] httr_1.4.7              purrr_1.0.2             fansi_1.0.6             UCSC.utils_1.0.0        Biostrings_2.72.1       httr2_1.0.3             cli_3.6.3               rlang_1.1.4            
[25] crayon_1.5.3            dbplyr_2.5.0            XVector_0.44.0          Biobase_2.64.0          bit64_4.0.5             withr_3.0.1             cachem_1.1.0            tools_4.4.1            
[33] memoise_2.0.1           dplyr_1.1.4             filelock_1.0.3          GenomeInfoDbData_1.2.12 BiocGenerics_0.50.0     curl_5.2.2              vctrs_0.6.5             R6_2.5.1               
[41] png_0.1-8               stats4_4.4.1            lifecycle_1.0.4         BiocFileCache_2.12.0    zlibbioc_1.50.0         KEGGREST_1.44.1         stringr_1.5.1           S4Vectors_0.42.1       
[49] IRanges_2.38.1          bit_4.0.5               pkgconfig_2.0.3         pillar_1.9.0            glue_1.7.0              tibble_3.2.1            tidyselect_1.2.1        rstudioapi_0.16.0      
[57] compiler_4.4.1          prettyunits_1.2.0
biomaRt • 875 views
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2
Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

I believe you want useMart for this use-case.

> ensembl <- useEnsembl("plants_mart", "zmays_eg_gene", host = "https://plants.ensembl.org")
Error in .getAttributes(mart, verbose = verbose) : 
  biomaRt error: looks like we're connecting to incompatible version of BioMart.
> mart <- useMart("plants_mart","zmays_eg_gene", host = "https://plants.ensembl.org")
> head(listAttributes(mart))
                   name
1       ensembl_gene_id
2 ensembl_transcript_id
3    ensembl_peptide_id
4       ensembl_exon_id
5           description
6       chromosome_name
               description
1           Gene stable ID
2     Transcript stable ID
3        Protein stable ID
4           Exon stable ID
5         Gene description
6 Chromosome/scaffold name
          page
1 feature_page
2 feature_page
3 feature_page
4 feature_page
5 feature_page
6 feature_page
0
Entering edit mode

This is amazing. Thank you so much

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