Introduction
OncoTree is a standardized classification system used in cancer research and clinical practice to categorize different types of cancer based on their tissue of origin, molecular characteristics, and other relevant factors. Developed by Memorial Sloan Kettering Cancer Center (MSK), OncoTree provides a hierarchical framework that organizes cancer types into a structured tree-like diagram.
- provides a standardized classification system for categorizing different types of cancer based on their tissue of origin, molecular characteristics, and other relevant factors.
- provides a hierarchical framework that organizes cancer types into a structured tree-like diagram.
- useful for ensuring consistency in how cancer types are classified and reported across different studies and clinical settings.
Licensing
OncoTree is licensed under CC BY 4.0. Source: https://github.com/cBioPortal/oncotree
Querying OncoTree
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 TumorSubtypes of a specific cancer type
The getCancerSubtypes function retrieves the subtypes of
a specific cancer type.
getOncotreeTumorTypes()
#> code color
#> <char> <char>
#> 1: PNS Gray
#> 2: LUNG Gainsboro
#> 3: PENIS Blue
#> 4: KIDNEY Orange
#> 5: STOMACH LightSkyBlue
#> ---
#> 893: BIALCL LimeGreen
#> 894: ALCLALKP LimeGreen
#> 895: ALCLALKN LimeGreen
#> 896: LYP LimeGreen
#> 897: PCALCL LimeGreen
#> name
#> <char>
#> 1: Peripheral Nervous System
#> 2: Lung
#> 3: Penis
#> 4: Kidney
#> 5: Esophagus/Stomach
#> ---
#> 893: Breast Implant-Associated Anaplastic Large-Cell Lymphoma
#> 894: Anaplastic Large-Cell Lymphoma ALK Positive
#> 895: Anaplastic Large-Cell Lymphoma ALK Negative
#> 896: Lymphomatoid Papulosis
#> 897: Primary Cutaneous Anaplastic Large Cell Lymphoma
#> mainType externalReferences tissue
#> <char> <list> <list>
#> 1: Peripheral Nervous System Cancer C0206417 C12465
#> 2: Lung Cancer C0024109 C12468
#> 3: Penile Cancer C0030851 C12409
#> 4: Kidney Cancer C0022646 C12415
#> 5: Esophageal/Stomach Cancer C0038351 C12391
#> ---
#> 893: Mature T and NK Neoplasms C4528210 C139012
#> 894: Mature T and NK Neoplasms C1332079 C37193
#> 895: Mature T and NK Neoplasms C1332078 C37194
#> 896: Mature T and NK Neoplasms C0206182 C3721
#> 897: Mature T and NK Neoplasms C1301362 C6860
#> children parent history level revocations precursors
#> <char> <char> <list> <int> <list> <list>
#> 1: Peripheral Nervous System TISSUE 1
#> 2: Lung TISSUE 1
#> 3: Penis TISSUE 1
#> 4: Kidney TISSUE 1
#> 5: Esophagus/Stomach TISSUE 1
#> ---
#> 893: Lymphoid ALCL 6
#> 894: Lymphoid ALCL 6
#> 895: Lymphoid ALCL 6
#> 896: Lymphoid PCLPD 6
#> 897: Lymphoid PCLPD 6
sessionInfo()
#> R version 4.5.3 (2026-03-11)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.4 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=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
#> [4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
#> [7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
#> [10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: UTC
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] AnnotationGx_0.99.3
#>
#> loaded via a namespace (and not attached):
#> [1] cli_3.6.6 knitr_1.51 rlang_1.2.0
#> [4] xfun_0.57 textshaping_1.0.5 jsonlite_2.0.0
#> [7] data.table_1.18.2.1 glue_1.8.1 backports_1.5.1
#> [10] htmltools_0.5.9 ragg_1.5.2 sass_0.4.10
#> [13] rappdirs_0.3.4 rmarkdown_2.31 evaluate_1.0.5
#> [16] jquerylib_0.1.4 fastmap_1.2.0 yaml_2.3.12
#> [19] lifecycle_1.0.5 httr2_1.2.2 memoise_2.0.1
#> [22] compiler_4.5.3 fs_2.1.0 systemfonts_1.3.2
#> [25] digest_0.6.39 R6_2.6.1 curl_7.0.0
#> [28] magrittr_2.0.5 bslib_0.10.0 checkmate_2.3.4
#> [31] tools_4.5.3 pkgdown_2.2.0 cachem_1.1.0
#> [34] desc_1.4.3