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: PLEURA Blue
#> 2: PERITONEUM Green
#> 3: PNS Gray
#> 4: UTERUS PeachPuff
#> 5: AMPULLA_OF_VATER Purple
#> ---
#> 893: BIALCL LimeGreen
#> 894: ALCLALKP LimeGreen
#> 895: ALCLALKN LimeGreen
#> 896: PCALCL LimeGreen
#> 897: LYP LimeGreen
#> name
#> <char>
#> 1: Pleura
#> 2: Peritoneum
#> 3: Peripheral Nervous System
#> 4: Uterus
#> 5: Ampulla of Vater
#> ---
#> 893: Breast Implant-Associated Anaplastic Large-Cell Lymphoma
#> 894: Anaplastic Large-Cell Lymphoma ALK Positive
#> 895: Anaplastic Large-Cell Lymphoma ALK Negative
#> 896: Primary Cutaneous Anaplastic Large Cell Lymphoma
#> 897: Lymphomatoid Papulosis
#> mainType externalReferences tissue
#> <char> <list> <list>
#> 1: Pleural Cancer C0032225 C12469
#> 2: Peritoneal Cancer C0031153 C12770
#> 3: Peripheral Nervous System Cancer C0206417 C12465
#> 4: Uterine Cancer C0042149 C12405
#> 5: Ampullary Carcinoma C0042425 C13011
#> ---
#> 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 C1301362 C6860
#> 897: Mature T and NK Neoplasms C0206182 C3721
#> children parent history level revocations precursors
#> <char> <char> <list> <int> <list> <list>
#> 1: Pleura TISSUE 1
#> 2: Peritoneum TISSUE 1
#> 3: Peripheral Nervous System TISSUE 1
#> 4: Uterus TISSUE 1
#> 5: Ampulla of Vater 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 4.6.0 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_0.99.7
#>
#> loaded via a namespace (and not attached):
#> [1] bit_4.6.0 jsonlite_2.0.0 crayon_1.5.3
#> [4] dplyr_1.2.1 compiler_4.6.0 filelock_1.0.3
#> [7] tidyselect_1.2.1 blob_1.3.0 parallel_4.6.0
#> [10] jquerylib_0.1.4 yaml_2.3.12 fastmap_1.2.0
#> [13] R6_2.6.1 generics_0.1.4 curl_7.0.0
#> [16] httr2_1.2.2 knitr_1.51 backports_1.5.1
#> [19] checkmate_2.3.4 tibble_3.3.1 DBI_1.3.0
#> [22] bslib_0.10.0 pillar_1.11.1 rlang_1.2.0
#> [25] cachem_1.1.0 xfun_0.57 sass_0.4.10
#> [28] bit64_4.8.0 otel_0.2.0 RSQLite_2.4.6
#> [31] memoise_2.0.1 cli_3.6.6 withr_3.0.2
#> [34] magrittr_2.0.5 digest_0.6.39 dbplyr_2.5.2
#> [37] rappdirs_0.3.4 lifecycle_1.0.5 BiocFileCache_3.1.0
#> [40] vctrs_0.7.3 evaluate_1.0.5 glue_1.8.1
#> [43] rmarkdown_2.31 purrr_1.2.2 tools_4.6.0
#> [46] pkgconfig_2.0.3 htmltools_0.5.9