AnnotationGx provides a set of functions for querying OncoTree to retrieve three types of information: - OncoTree release versions - Main Cancer types - Subtypes of a specific cancer type and their relationships
OncoTree release versions
The getOncotreeVersions function retrieves the available OncoTree release.
getOncotreeVersions()
#> api_identifier
#> <char>
#> 1: oncotree_latest_stable
#> 2: oncotree_2025_10_03
#> 3: oncotree_2025_04_08
#> 4: oncotree_development
#> 5: oncotree_candidate_release
#> 6: oncotree_2021_11_02
#> 7: oncotree_2020_10_01
#> 8: oncotree_2020_04_01
#> 9: oncotree_2020_02_06
#> 10: oncotree_2020_02_01
#> 11: oncotree_2019_12_01
#> 12: oncotree_2019_08_01
#> 13: oncotree_2019_05_01
#> 14: oncotree_2019_03_01
#> 15: oncotree_2019_02_01
#> 16: oncotree_2018_11_01
#> 17: oncotree_2018_09_01
#> 18: oncotree_2018_08_01
#> 19: oncotree_2018_07_01
#> 20: oncotree_2018_06_15
#> 21: oncotree_2018_06_01
#> 22: oncotree_2018_05_01
#> 23: oncotree_2018_04_01
#> 24: oncotree_2018_03_01
#> 25: oncotree_2018_02_01
#> 26: oncotree_2018_01_01
#> 27: oncotree_2017_11_01
#> 28: oncotree_2017_10_05
#> 29: oncotree_2017_06_21
#> 30: oncotree_legacy_1.1
#> api_identifier
#> <char>
#> description
#> <char>
#> 1: This is the latest approved version for public use.
#> 2: Stable OncoTree released on date 2025-10-03
#> 3: Stable OncoTree released on date 2025-04-08
#> 4: Latest OncoTree under development (subject to <b class=text-danger>change without notice</b>)
#> 5: This version of the OncoTree reflects upcoming changes which have been approved for the next public release of oncotree. It also includes a small number of nodes which will not be included in the next public release (see the news page for more details). The next public release may possibly include additional oncotree nodes, if approved.
#> 6: Stable OncoTree released on date 2021-11-02
#> 7: Stable OncoTree released on date 2020-10-01
#> 8: Stable OncoTree released on date 2020-04-01
#> 9: Stable OncoTree released on date 2020-02-06
#> 10: Stable OncoTree released on date 2020-02-01
#> 11: Stable OncoTree released on date 2019-12-01
#> 12: Stable OncoTree released on date 2019-08-01
#> 13: Stable OncoTree released on date 2019-05-01
#> 14: Stable OncoTree released on date 2019-03-01
#> 15: Stable OncoTree released on date 2019-02-01
#> 16: Stable OncoTree released on date 2018-11-01
#> 17: Stable OncoTree released on date 2018-09-01
#> 18: Stable OncoTree released on date 2018-08-01
#> 19: Stable OncoTree released on date 2018-07-01
#> 20: Stable OncoTree released on date 2018-06-15
#> 21: Stable OncoTree released on date 2018-06-01
#> 22: Stable OncoTree released on date 2018-05-01
#> 23: Stable OncoTree released on date 2018-04-01
#> 24: Stable OncoTree released on date 2018-03-01
#> 25: Stable OncoTree released on date 2018-02-01
#> 26: Stable OncoTree released on date 2018-01-01
#> 27: Stable OncoTree released on date 2017-11-01
#> 28: Stable OncoTree released on date 2017-10-05
#> 29: Stable OncoTree released on date 2017-06-21
#> 30: This is the closest match in TopBraid for the TumorTypes_txt file associated with release 1.1 of OncoTree (approved by committee)
#> description
#> <char>
#> release_date visible
#> <char> <lgcl>
#> 1: 2025-10-03 TRUE
#> 2: 2025-10-03 FALSE
#> 3: 2025-04-08 FALSE
#> 4: 2021-11-04 TRUE
#> 5: 2021-11-03 TRUE
#> 6: 2021-11-02 FALSE
#> 7: 2020-10-01 FALSE
#> 8: 2020-04-01 FALSE
#> 9: 2020-02-06 FALSE
#> 10: 2020-02-01 FALSE
#> 11: 2019-12-01 FALSE
#> 12: 2019-08-01 FALSE
#> 13: 2019-05-01 FALSE
#> 14: 2019-03-01 FALSE
#> 15: 2019-02-01 FALSE
#> 16: 2018-11-01 FALSE
#> 17: 2018-09-01 FALSE
#> 18: 2018-08-01 FALSE
#> 19: 2018-07-01 FALSE
#> 20: 2018-06-15 FALSE
#> 21: 2018-06-01 FALSE
#> 22: 2018-05-01 FALSE
#> 23: 2018-04-01 FALSE
#> 24: 2018-03-01 FALSE
#> 25: 2018-02-01 FALSE
#> 26: 2018-01-01 FALSE
#> 27: 2017-11-01 FALSE
#> 28: 2017-10-05 FALSE
#> 29: 2017-06-21 FALSE
#> 30: 2016-03-28 FALSE
#> release_date visible
#> <char> <lgcl>
Main Cancer types
The getMainCancerTypes function retrieves the main cancer types in OncoTree.
getOncotreeMainTypes()
#> mainType
#> <char>
#> 1: Adenocarcinoma In Situ
#> 2: Adenocarcinoma in Retrorectal Cystic Hamartoma
#> 3: Adrenal Gland Cancer
#> 4: Adrenocortical Adenoma
#> 5: Adrenocortical Carcinoma
#> ---
#> 116: Uterine Sarcoma
#> 117: Vaginal Cancer
#> 118: Vulvar Carcinoma
#> 119: Vulvar/Vaginal Cancer
#> 120: Wilms Tumor
Subtypes of a specific cancer type
The getCancerSubtypes function retrieves the subtypes of a specific cancer type.
getOncotreeTumorTypes()
#> code color
#> <char> <char>
#> 1: BREAST HotPink
#> 2: BLADDER Yellow
#> 3: STOMACH LightSkyBlue
#> 4: PANCREAS Purple
#> 5: PENIS Blue
#> ---
#> 893: PCALCL LimeGreen
#> 894: LYP LimeGreen
#> 895: ALCLALKP LimeGreen
#> 896: ALCLALKN LimeGreen
#> 897: BIALCL LimeGreen
#> name
#> <char>
#> 1: Breast
#> 2: Bladder/Urinary Tract
#> 3: Esophagus/Stomach
#> 4: Pancreas
#> 5: Penis
#> ---
#> 893: Primary Cutaneous Anaplastic Large Cell Lymphoma
#> 894: Lymphomatoid Papulosis
#> 895: Anaplastic Large-Cell Lymphoma ALK Positive
#> 896: Anaplastic Large-Cell Lymphoma ALK Negative
#> 897: Breast Implant-Associated Anaplastic Large-Cell Lymphoma
#> mainType externalReferences tissue
#> <char> <list> <list>
#> 1: Breast Cancer C0006141 C12971
#> 2: Bladder/Urinary Tract Cancer C0005682 C12414
#> 3: Esophageal/Stomach Cancer C0038351 C12391
#> 4: Pancreatic Cancer C0030274 C12393
#> 5: Penile Cancer C0030851 C12409
#> ---
#> 893: Mature T and NK Neoplasms C1301362 C6860
#> 894: Mature T and NK Neoplasms C0206182 C3721
#> 895: Mature T and NK Neoplasms C1332079 C37193
#> 896: Mature T and NK Neoplasms C1332078 C37194
#> 897: Mature T and NK Neoplasms C4528210 C139012
#> children parent history level revocations precursors
#> <char> <char> <list> <int> <list> <list>
#> 1: Breast TISSUE 1
#> 2: Bladder/Urinary Tract TISSUE 1
#> 3: Esophagus/Stomach TISSUE 1
#> 4: Pancreas TISSUE 1
#> 5: Penis TISSUE 1
#> ---
#> 893: Lymphoid PCLPD 6
#> 894: Lymphoid PCLPD 6
#> 895: Lymphoid ALCL 6
#> 896: Lymphoid ALCL 6
#> 897: Lymphoid ALCL 6
sessionInfo()
#> R version 4.6.0 alpha (2026-04-05 r89794)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.4 LTS
#>
#> Matrix products: default
#> BLAS: /home/biocbuild/bbs-3.23-bioc/R/lib/libRblas.so
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
#> [3] LC_TIME=en_GB LC_COLLATE=C
#> [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: America/New_York
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] data.table_1.18.2.1 AnnotationGx_0.99.2
#>
#> loaded via a namespace (and not attached):
#> [1] crayon_1.5.3 cli_3.6.6 knitr_1.51 rlang_1.2.0
#> [5] xfun_0.57 otel_0.2.0 jsonlite_2.0.0 glue_1.8.1
#> [9] backports_1.5.1 htmltools_0.5.9 sass_0.4.10 rappdirs_0.3.4
#> [13] rmarkdown_2.31 evaluate_1.0.5 jquerylib_0.1.4 fastmap_1.2.0
#> [17] yaml_2.3.12 lifecycle_1.0.5 httr2_1.2.2 memoise_2.0.1
#> [21] compiler_4.6.0 digest_0.6.39 R6_2.6.1 curl_7.0.0
#> [25] parallel_4.6.0 magrittr_2.0.5 bslib_0.10.0 checkmate_2.3.4
#> [29] withr_3.0.2 tools_4.6.0 cachem_1.1.0