Last updated: 2025-07-11
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 6a48046 | Dave Tang | 2025-07-11 | Using biomaRt with rat |
The biomaRt package provides an interface to BioMart databases provided by Ensembl.
biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite. The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are maintain by Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.
For more information, check out the Accessing Ensembl annotation with biomaRt guide.
To begin, install the {biomaRt} package.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("biomaRt")Load package.
packageVersion("biomaRt")[1] '2.64.0'suppressPackageStartupMessages(library(biomaRt))Connect to the selected BioMart database and rat dataset.
ensembl <- useMart("ensembl", dataset='rnorvegicus_gene_ensembl')
ensemblObject of class 'Mart':
Using the ENSEMBL_MART_ENSEMBL BioMart database
Using the rnorvegicus_gene_ensembl datasetENSRNOG00000031780 should be associated to:
my_gene <- 'ENSRNOG00000031780'
getBM(
attributes=c('ensembl_gene_id', 'go_id'),
filters="ensembl_gene_id",
values = my_gene,
mart = ensembl
) ensembl_gene_id go_id
1 ENSRNOG00000031780 GO:0006412
2 ENSRNOG00000031780 GO:0030533ENSRNOG00000030644.
my_gene <- 'ENSRNOG00000030644'
expected_go <- c('GO:0001666', 'GO:0003954', 'GO:0005739', 'GO:0005743', 'GO:0006120', 'GO:0008137', 'GO:0009060', 'GO:0009410', 'GO:0016020', 'GO:0030425', 'GO:0031966', 'GO:0032981', 'GO:0033194', 'GO:0043025', 'GO:0045271', 'GO:1902600')
getBM(
attributes=c('ensembl_gene_id', 'go_id'),
filters="ensembl_gene_id",
values = my_gene,
mart = ensembl
) -> observed_go
expected_go %in% observed_go$go_id [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[16] TRUEobserved_go$go_id %in% expected_go [1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
[16] TRUE
sessionInfo()R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.64.0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] KEGGREST_1.48.1 xfun_0.52 bslib_0.9.0
[4] httr2_1.1.2 processx_3.8.6 Biobase_2.68.0
[7] callr_3.7.6 vctrs_0.6.5 tools_4.5.0
[10] ps_1.9.1 generics_0.1.4 curl_6.4.0
[13] stats4_4.5.0 tibble_3.3.0 AnnotationDbi_1.70.0
[16] RSQLite_2.4.1 blob_1.2.4 pkgconfig_2.0.3
[19] dbplyr_2.5.0 S4Vectors_0.46.0 lifecycle_1.0.4
[22] GenomeInfoDbData_1.2.14 compiler_4.5.0 stringr_1.5.1
[25] git2r_0.36.2 Biostrings_2.76.0 progress_1.2.3
[28] getPass_0.2-4 httpuv_1.6.16 GenomeInfoDb_1.44.0
[31] htmltools_0.5.8.1 sass_0.4.10 yaml_2.3.10
[34] later_1.4.2 pillar_1.11.0 crayon_1.5.3
[37] jquerylib_0.1.4 whisker_0.4.1 cachem_1.1.0
[40] tidyselect_1.2.1 digest_0.6.37 stringi_1.8.7
[43] purrr_1.0.4 dplyr_1.1.4 rprojroot_2.0.4
[46] fastmap_1.2.0 cli_3.6.5 magrittr_2.0.3
[49] withr_3.0.2 filelock_1.0.3 prettyunits_1.2.0
[52] UCSC.utils_1.4.0 promises_1.3.3 rappdirs_0.3.3
[55] bit64_4.6.0-1 rmarkdown_2.29 XVector_0.48.0
[58] httr_1.4.7 bit_4.6.0 png_0.1-8
[61] hms_1.1.3 memoise_2.0.1 evaluate_1.0.4
[64] knitr_1.50 IRanges_2.42.0 BiocFileCache_2.16.0
[67] rlang_1.1.6 Rcpp_1.1.0 glue_1.8.0
[70] DBI_1.2.3 xml2_1.3.8 BiocGenerics_0.54.0
[73] rstudioapi_0.17.1 jsonlite_2.0.0 R6_2.6.1
[76] fs_1.6.6