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 name
#> <char> <char> <char>
#> 1: THYMUS Purple Thymus
#> 2: PENIS Blue Penis
#> 3: UTERUS PeachPuff Uterus
#> 4: PLEURA Blue Pleura
#> 5: LIVER MediumSeaGreen Liver
#> ---
#> 893: ISFN LimeGreen In Situ Follicular Neoplasia
#> 894: DFL LimeGreen Duodenal-Type Follicular Lymphoma
#> 895: ISMCL LimeGreen In Situ Mantle Cell Neoplasia
#> 896: ABC LimeGreen Activated B-cell Type
#> 897: GCB LimeGreen Germinal Center B-Cell Type
#> mainType externalReferences tissue children parent
#> <char> <list> <list> <char> <char>
#> 1: Thymic Cancer C0040113 C12433 Thymus TISSUE
#> 2: Penile Cancer C0030851 C12409 Penis TISSUE
#> 3: Uterine Cancer C0042149 C12405 Uterus TISSUE
#> 4: Pleural Cancer C0032225 C12469 Pleura TISSUE
#> 5: Liver Cancer C0023884 C12392 Liver TISSUE
#> ---
#> 893: Mature B-Cell Neoplasms C4524188 C138181 Lymphoid FL
#> 894: Mature B-Cell Neoplasms C4524187 C138185 Lymphoid FL
#> 895: Mature B-Cell Neoplasms C4527429 C138191 Lymphoid MCL
#> 896: Mature B-Cell Neoplasms [NULL] [NULL] Lymphoid DLBCLNOS
#> 897: Mature B-Cell Neoplasms C1333295 C36080 Lymphoid DLBCLNOS
#> history level revocations precursors
#> <list> <int> <list> <list>
#> 1: 1
#> 2: 1
#> 3: 1
#> 4: 1
#> 5: 1
#> ---
#> 893: 6
#> 894: 6
#> 895: 6
#> 896: 6
#> 897: 6
sessionInfo()
#> R version 4.6.0 RC (2026-04-17 r89917)
#> 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_0.99.6
#>
#> 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