Accessing the OncoKB API with oncoKBData
May 09, 2025
Source:vignettes/oncoKBData.Rmd
oncoKBData.RmdoncoKBData
The aim of the package is to expose the OncoKB API through an R client. This vignette demonstrates public API access. To learn more about the OncoKB database, visit https://www.oncokb.org.
Installation
To get the development version of oncoKBData use:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("waldronlab/oncoKBData")Introduction
The oncoKBData aims to provide access to the OncoKB API
via the public API. Access is also possible with a licensed token.
API representation
In order to use the OncoKB API, we must instantiate an API object as provided by the rapiclient and AnVIL packages.
oncokb <- oncoKB()Note that for private API access, users must change the
api. argument in the oncoKB function.
Operations
Check available tags, operations, and descriptions as a
tibble:
tags(oncokb)## # A tibble: 20 × 3
## tag operation summary
## <chr> <chr> <chr>
## 1 Annotations annotateCopyNumberAlterationsGetUsingGET_1 annotateCopyNum…
## 2 Annotations annotateCopyNumberAlterationsPostUsingPOST_1 annotateCopyNum…
## 3 Annotations annotateMutationsByGenomicChangeGetUsingGET_1 annotateMutatio…
## 4 Annotations annotateMutationsByGenomicChangePostUsingPOST_1 annotateMutatio…
## 5 Annotations annotateMutationsByHGVSgGetUsingGET_1 annotateMutatio…
## 6 Annotations annotateMutationsByHGVSgPostUsingPOST_1 annotateMutatio…
## 7 Annotations annotateMutationsByProteinChangeGetUsingGET_1 annotateMutatio…
## 8 Annotations annotateMutationsByProteinChangePostUsingPOST_1 annotateMutatio…
## 9 Annotations annotateStructuralVariantsGetUsingGET_1 annotateStructu…
## 10 Annotations annotateStructuralVariantsPostUsingPOST_1 annotateStructu…
## 11 Cancer Genes utilsAllCuratedGenesGetUsingGET_1 utilsAllCurated…
## 12 Cancer Genes utilsAllCuratedGenesTxtGetUsingGET_1 utilsAllCurated…
## 13 Cancer Genes utilsCancerGeneListGetUsingGET_1 utilsCancerGene…
## 14 Cancer Genes utilsCancerGeneListTxtGetUsingGET_1 utilsCancerGene…
## 15 Info infoGetUsingGET_1 infoGet
## 16 Levels levelsDiagnosticGetUsingGET_1 levelsDiagnosti…
## 17 Levels levelsGetUsingGET_1 levelsGet
## 18 Levels levelsPrognosticGetUsingGET_1 levelsPrognosti…
## 19 Levels levelsResistanceGetUsingGET_1 levelsResistanc…
## 20 Levels levelsSensitiveGetUsingGET_1 levelsSensitive…## [1] "annotateCopyNumberAlterationsGetUsingGET_1"
## [2] "annotateCopyNumberAlterationsPostUsingPOST_1"
## [3] "annotateMutationsByGenomicChangeGetUsingGET_1"
## [4] "annotateMutationsByGenomicChangePostUsingPOST_1"
## [5] "annotateMutationsByHGVSgGetUsingGET_1"
## [6] "annotateMutationsByHGVSgPostUsingPOST_1"Note. The annotations API access requires a token.
Levels of Evidence
To retrieve the levels of evidence for all types (i.e.,
‘therapeutic’, ‘diagnostic’, ‘prognostic’, and ‘FDA’) run the
levelsOfEvidence function.
(loe <- levelsOfEvidence(oncokb))## DataFrame with 16 rows and 4 columns
## levelOfEvidence description htmlDescription colorHex
## <character> <character> <character> <character>
## 1 LEVEL_1 FDA-recognized bioma.. <span><b>FDA-recogni.. #33A02C
## 2 LEVEL_2 Standard care biomar.. <span><b>Standard ca.. #1F78B4
## 3 LEVEL_3A Compelling clinical .. <span><b>Compelling .. #984EA3
## 4 LEVEL_3B Standard care or inv.. <span><b>Standard ca.. #BE98CE
## 5 LEVEL_4 Compelling biologica.. <span><b>Compelling .. #424242
## ... ... ... ... ...
## 12 LEVEL_Px1 FDA and/or professio.. <span><b>FDA and/or .. #33A02C
## 13 LEVEL_Px2 FDA and/or professio.. <span><b>FDA and/or .. #1F78B4
## 14 LEVEL_Px3 Biomarker is prognos.. <span>Biomarker is p.. #984EA3
## 15 LEVEL_R1 Standard care biomar.. <span><b>Standard of.. #EE3424
## 16 LEVEL_R2 Compelling clinical .. <span><b>Compelling .. #F79A92It will return a DataFrame with important
metadata:
## [1] "oncoTreeVersion" "ncitVersion" "dataVersion" "appVersion"
## [5] "apiVersion" "publicInstance" "genomeNexus"
metadata(loe)["oncoTreeVersion"]## $oncoTreeVersion
## [1] "oncotree_2019_12_01"
metadata(loe)[["apiVersion"]]## $version
## [1] "v1.5.0"
##
## $major
## [1] 1
##
## $minor
## [1] 5
##
## $patch
## [1] 0
##
## $suffixTokens
## list()
##
## $stable
## [1] TRUEGene tables
The API allows retrieval of curated genes where there is a single gene per observation:
curatedGenes(oncokb)## # A tibble: 933 × 13
## grch37Isoform grch37RefSeq grch38Isoform grch38RefSeq entrezGeneId hugoSymbol
## <chr> <chr> <chr> <chr> <int> <chr>
## 1 ENST00000265… NM_000927.4 ENST00000622… NM_00134894… 5243 ABCB1
## 2 ENST00000318… NM_005157.4 ENST00000318… NM_005157.4 25 ABL1
## 3 ENST00000502… NM_007314.3 ENST00000502… NM_007314.3 27 ABL2
## 4 ENST00000321… NM_139076.2 ENST00000321… NM_139076.2 84142 ABRAXAS1
## 5 ENST00000272… NM_020311 ENST00000272… NM_020311 57007 ACKR3
## 6 ENST00000331… NM_00119995… ENST00000573… NM_00119995… 71 ACTG1
## 7 ENST00000263… NM_00111106… ENST00000263… NM_00111106… 90 ACVR1
## 8 ENST00000257… NM_004302 ENST00000257… NM_004302 91 ACVR1B
## 9 ENST00000241… NM_001278579 ENST00000241… NM_001278579 92 ACVR2A
## 10 ENST00000381… NM_018702.3 ENST00000381… NM_018702.4 105 ADARB2
## # ℹ 923 more rows
## # ℹ 7 more variables: oncogene <lgl>, highestSensitiveLevel <chr>,
## # highestResistanceLevel <chr>, summary <chr>, background <chr>, tsg <lgl>,
## # highestResistancLevel <chr>and a long list of genes associated with cancer where there can be
multiple entries for the same hugoSymbol due to multiple
geneAliases:
cancerGeneList(oncokb)## # A tibble: 3,275 × 17
## hugoSymbol entrezGeneId grch37Isoform grch37RefSeq grch38Isoform grch38RefSeq
## <chr> <int> <chr> <chr> <chr> <chr>
## 1 ABL1 25 ENST00000318… NM_005157.4 ENST00000318… NM_005157.4
## 2 ABL1 25 ENST00000318… NM_005157.4 ENST00000318… NM_005157.4
## 3 ABL1 25 ENST00000318… NM_005157.4 ENST00000318… NM_005157.4
## 4 AKT1 207 ENST00000349… NM_00101443… ENST00000349… NM_00101443…
## 5 AKT1 207 ENST00000349… NM_00101443… ENST00000349… NM_00101443…
## 6 AKT1 207 ENST00000349… NM_00101443… ENST00000349… NM_00101443…
## 7 AKT1 207 ENST00000349… NM_00101443… ENST00000349… NM_00101443…
## 8 AKT1 207 ENST00000349… NM_00101443… ENST00000349… NM_00101443…
## 9 ALK 238 ENST00000389… NM_004304.4 ENST00000389… NM_004304.4
## 10 AMER1 139285 ENST00000330… NM_152424.3 ENST00000374… NM_152424.3
## # ℹ 3,265 more rows
## # ℹ 11 more variables: oncokbAnnotated <lgl>, occurrenceCount <int>,
## # mSKImpact <lgl>, mSKHeme <lgl>, foundation <lgl>, foundationHeme <lgl>,
## # vogelstein <lgl>, sangerCGC <lgl>, geneAliases <list>, tsg <lgl>,
## # oncogene <lgl>Session Information
Click to expand 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] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] S4Vectors_0.47.0 BiocGenerics_0.55.0 generics_0.1.3
[4] oncoKBData_0.99.7 AnVIL_1.21.3 AnVILBase_1.3.1
[7] dplyr_1.1.4 BiocStyle_2.37.0
loaded via a namespace (and not attached):
[1] utf8_1.2.5 rappdirs_0.3.3 sass_0.4.10
[4] futile.options_1.0.1 digest_0.6.37 magrittr_2.0.3
[7] evaluate_1.0.3 bookdown_0.43 fastmap_1.2.0
[10] jsonlite_2.0.0 formatR_1.14 promises_1.3.2
[13] BiocManager_1.30.25 httr_1.4.7 rapiclient_0.1.8
[16] codetools_0.2-20 httr2_1.1.2 textshaping_1.0.1
[19] jquerylib_0.1.4 cli_3.6.5 shiny_1.10.0
[22] rlang_1.1.6 futile.logger_1.4.3 cachem_1.1.0
[25] yaml_2.3.10 BiocBaseUtils_1.11.0 tools_4.5.0
[28] httpuv_1.6.16 DT_0.33 lambda.r_1.2.4
[31] curl_6.2.2 vctrs_0.6.5 R6_2.6.1
[34] mime_0.13 lifecycle_1.0.4 fs_1.6.6
[37] htmlwidgets_1.6.4 miniUI_0.1.2 ragg_1.4.0
[40] pkgconfig_2.0.3 desc_1.4.3 pkgdown_2.1.2
[43] pillar_1.10.2 bslib_0.9.0 later_1.4.2
[46] glue_1.8.0 Rcpp_1.0.14 systemfonts_1.2.3
[49] xfun_0.52 tibble_3.2.1 tidyselect_1.2.1
[52] knitr_1.50 xtable_1.8-4 htmltools_0.5.8.1
[55] rmarkdown_2.29 compiler_4.5.0