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.
To get the development version of oncoKBData use:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("waldronlab/oncoKBData")library(oncoKBData)
library(S4Vectors)The oncoKBData aims to provide access to the OncoKB API via the public
API. Access is also possible with a licensed token.
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.
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 annotateCopyNumberAlterationsGet
#> 2 Annotations annotateCopyNumberAlterationsPostUsingPOST_1 annotateCopyNumberAlterationsPost
#> 3 Annotations annotateMutationsByGenomicChangeGetUsingGET_1 annotateMutationsByGenomicChangeGet
#> 4 Annotations annotateMutationsByGenomicChangePostUsingPOST_1 annotateMutationsByGenomicChangePost
#> 5 Annotations annotateMutationsByHGVSgGetUsingGET_1 annotateMutationsByHGVSgGet
#> 6 Annotations annotateMutationsByHGVSgPostUsingPOST_1 annotateMutationsByHGVSgPost
#> 7 Annotations annotateMutationsByProteinChangeGetUsingGET_1 annotateMutationsByProteinChangeGet
#> 8 Annotations annotateMutationsByProteinChangePostUsingPOST_1 annotateMutationsByProteinChangePost
#> 9 Annotations annotateStructuralVariantsGetUsingGET_1 annotateStructuralVariantsGet
#> 10 Annotations annotateStructuralVariantsPostUsingPOST_1 annotateStructuralVariantsPost
#> 11 Cancer Genes utilsAllCuratedGenesGetUsingGET_1 utilsAllCuratedGenesGet
#> 12 Cancer Genes utilsAllCuratedGenesTxtGetUsingGET_1 utilsAllCuratedGenesTxtGet
#> 13 Cancer Genes utilsCancerGeneListGetUsingGET_1 utilsCancerGeneListGet
#> 14 Cancer Genes utilsCancerGeneListTxtGetUsingGET_1 utilsCancerGeneListTxtGet
#> 15 Info infoGetUsingGET_1 infoGet
#> 16 Levels levelsDiagnosticGetUsingGET_1 levelsDiagnosticGet
#> 17 Levels levelsGetUsingGET_1 levelsGet
#> 18 Levels levelsPrognosticGetUsingGET_1 levelsPrognosticGet
#> 19 Levels levelsResistanceGetUsingGET_1 levelsResistanceGet
#> 20 Levels levelsSensitiveGetUsingGET_1 levelsSensitiveGet
head(tags(oncokb)$operation)
#> [1] "annotateCopyNumberAlterationsGetUsingGET_1" "annotateCopyNumberAlterationsPostUsingPOST_1"
#> [3] "annotateMutationsByGenomicChangeGetUsingGET_1" "annotateMutationsByGenomicChangePostUsingPOST_1"
#> [5] "annotateMutationsByHGVSgGetUsingGET_1" "annotateMutationsByHGVSgPostUsingPOST_1"Note. The annotations API access requires a token.
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:
names(metadata(loe))
#> [1] "oncoTreeVersion" "ncitVersion" "dataVersion" "appVersion" "apiVersion" "publicInstance"
metadata(loe)["oncoTreeVersion"]
#> $oncoTreeVersion
#> [1] "oncotree_2019_12_01"
metadata(loe)[["apiVersion"]]
#> $version
#> [1] "v1.4.0"
#>
#> $major
#> [1] 1
#>
#> $minor
#> [1] 4
#>
#> $patch
#> [1] 0
#>
#> $suffixTokens
#> list()
#>
#> $stable
#> [1] TRUEThe API allows retrieval of curated genes where there is a single gene per observation:
curatedGenes(oncokb)
#> # A tibble: 725 × 13
#> grch37Isoform grch37RefSeq grch38Isoform grch38RefSeq entrezGeneId hugoSymbol oncogene highest…¹ highe…² summary backg…³ tsg highe…⁴
#> <chr> <chr> <chr> <chr> <int> <chr> <lgl> <chr> <chr> <chr> <chr> <lgl> <chr>
#> 1 ENST00000318560 NM_005157.4 ENST00000318560 NM_005157.4 25 ABL1 TRUE "1" "R1" ABL1, … "ABL1 … FALSE "R1"
#> 2 ENST00000502732 NM_007314.3 ENST00000502732 NM_007314.3 27 ABL2 TRUE "" "" ABL2, … "ABL2 … FALSE ""
#> 3 ENST00000321945 NM_139076.2 ENST00000321945 NM_139076.2 84142 ABRAXAS1 FALSE "" "" ABRAXA… "The A… TRUE ""
#> 4 ENST00000331925 NM_001199954.1 ENST00000573283 NM_001199954.1 71 ACTG1 FALSE "" "" ACTG1,… "ACTG1… TRUE ""
#> 5 ENST00000263640 NM_001111067.2 ENST00000263640 NM_001111067.2 90 ACVR1 TRUE "" "" ACVR1,… "ACVR1… FALSE ""
#> 6 ENST00000396623 NM_144650 ENST00000396623 NM_144650 137872 ADHFE1 TRUE "" "" ADHFE1… "ADHFE… FALSE ""
#> 7 ENST00000265343 NM_014423 ENST00000265343 NM_014423 27125 AFF4 TRUE "" "" AFF4, … "AFF4 … FALSE ""
#> 8 ENST00000373204 NM_012199.2 ENST00000373204 NM_012199.2 26523 AGO1 TRUE "" "" AGO1, … "AGO1 … FALSE ""
#> 9 ENST00000220592 NM_012154.3 ENST00000220592 NM_012154.3 27161 AGO2 FALSE "" "" AGO2, … "AGO2 … FALSE ""
#> 10 ENST00000262713 NM_032876.5 ENST00000262713 NM_032876.5 84962 AJUBA FALSE "" "" AJUBA,… "AJUBA… TRUE ""
#> # … with 715 more rows, and abbreviated variable names ¹highestSensitiveLevel, ²highestResistanceLevel, ³background, ⁴highestResistancLeveland 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: 3,019 × 17
#> hugoSymbol entrezGeneId grch37…¹ grch3…² grch3…³ grch3…⁴ oncok…⁵ occur…⁶ mSKIm…⁷ mSKHeme found…⁸ found…⁹ vogel…˟ sange…˟ geneA…˟ tsg oncog…˟
#> <chr> <int> <chr> <chr> <chr> <chr> <lgl> <int> <lgl> <lgl> <lgl> <lgl> <lgl> <lgl> <list> <lgl> <lgl>
#> 1 ABL1 25 ENST000… NM_005… ENST00… NM_005… TRUE 7 TRUE TRUE TRUE TRUE TRUE TRUE <chr> FALSE TRUE
#> 2 ABL1 25 ENST000… NM_005… ENST00… NM_005… TRUE 7 TRUE TRUE TRUE TRUE TRUE TRUE <chr> FALSE TRUE
#> 3 ABL1 25 ENST000… NM_005… ENST00… NM_005… TRUE 7 TRUE TRUE TRUE TRUE TRUE TRUE <chr> FALSE TRUE
#> 4 AKT1 207 ENST000… NM_001… ENST00… NM_001… TRUE 7 TRUE TRUE TRUE TRUE TRUE TRUE <chr> FALSE TRUE
#> 5 AKT1 207 ENST000… NM_001… ENST00… NM_001… TRUE 7 TRUE TRUE TRUE TRUE TRUE TRUE <chr> FALSE TRUE
#> 6 AKT1 207 ENST000… NM_001… ENST00… NM_001… TRUE 7 TRUE TRUE TRUE TRUE TRUE TRUE <chr> FALSE TRUE
#> 7 AKT1 207 ENST000… NM_001… ENST00… NM_001… TRUE 7 TRUE TRUE TRUE TRUE TRUE TRUE <chr> FALSE TRUE
#> 8 AKT1 207 ENST000… NM_001… ENST00… NM_001… TRUE 7 TRUE TRUE TRUE TRUE TRUE TRUE <chr> FALSE TRUE
#> 9 ALK 238 ENST000… NM_004… ENST00… NM_004… TRUE 7 TRUE TRUE TRUE TRUE TRUE TRUE <chr> FALSE TRUE
#> 10 AMER1 139285 ENST000… NM_152… ENST00… NM_152… TRUE 7 TRUE TRUE TRUE TRUE TRUE TRUE <chr> TRUE FALSE
#> # … with 3,009 more rows, and abbreviated variable names ¹grch37Isoform, ²grch37RefSeq, ³grch38Isoform, ⁴grch38RefSeq, ⁵oncokbAnnotated,
#> # ⁶occurrenceCount, ⁷mSKImpact, ⁸foundation, ⁹foundationHeme, ˟vogelstein, ˟sangerCGC, ˟geneAliases, ˟oncogenesessionInfo()
#> R Under development (unstable) (2023-02-22 r83892)
#> Platform: x86_64-pc-linux-gnu (64-bit)
#> Running under: Ubuntu 22.04.1 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-r0.3.20.so; LAPACK version 3.10.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
#> [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C 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 base
#>
#> other attached packages:
#> [1] BiocStyle_2.27.1 S4Vectors_0.37.4 BiocGenerics_0.45.0 oncoKBData_0.99.1 AnVIL_1.11.3 dplyr_1.1.0 colorout_1.2-2
#>
#> loaded via a namespace (and not attached):
#> [1] utf8_1.2.3 generics_0.1.3 tidyr_1.3.0 futile.options_1.0.1 digest_0.6.31 magrittr_2.0.3
#> [7] evaluate_0.20 fastmap_1.1.1 jsonlite_1.8.4 DBI_1.1.3 formatR_1.14 promises_1.2.0.1
#> [13] BiocManager_1.30.20 httr_1.4.5 purrr_1.0.1 fansi_1.0.4 rapiclient_0.1.3 codetools_0.2-19
#> [19] cli_3.6.0 shiny_1.7.4 rlang_1.0.6 futile.logger_1.4.3 ellipsis_0.3.2 withr_2.5.0
#> [25] yaml_2.3.7 tools_4.3.0 parallel_4.3.0 httpuv_1.6.9 DT_0.27 lambda.r_1.2.4
#> [31] curl_5.0.0 vctrs_0.5.2 R6_2.5.1 mime_0.12 lifecycle_1.0.3 htmlwidgets_1.6.1
#> [37] miniUI_0.1.1.1 pkgconfig_2.0.3 pillar_1.8.1 later_1.3.0 glue_1.6.2 Rcpp_1.0.10
#> [43] xfun_0.37 tibble_3.1.8 tidyselect_1.2.0 rstudioapi_0.14 knitr_1.42 xtable_1.8-4
#> [49] htmltools_0.5.4 rmarkdown_2.20 compiler_4.3.0