Querying OncoTree
OncoTree.RmdIntroduction
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 the National Cancer Institute (NCI) within the United States, 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.
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_2017_11_01
#> 2: oncotree_2020_10_01
#> 3: oncotree_2020_02_06
#> 4: oncotree_2019_12_01
#> 5: oncotree_2018_07_01
#> 6: oncotree_2017_06_21
#> 7: oncotree_2018_08_01
#> 8: oncotree_2017_10_05
#> 9: oncotree_2019_08_01
#> 10: oncotree_2018_09_01
#> 11: oncotree_2018_06_01
#> 12: oncotree_2018_03_01
#> 13: oncotree_2018_04_01
#> 14: oncotree_2018_05_01
#> 15: oncotree_2018_02_01
#> 16: oncotree_2019_05_01
#> 17: oncotree_legacy_1.1
#> 18: oncotree_2018_01_01
#> 19: oncotree_2018_06_15
#> 20: oncotree_2019_02_01
#> 21: oncotree_2020_04_01
#> 22: oncotree_2019_03_01
#> 23: oncotree_2020_02_01
#> 24: oncotree_2021_11_02
#> 25: oncotree_development
#> 26: oncotree_latest_stable
#> 27: oncotree_2018_11_01
#> 28: oncotree_candidate_release
#> api_identifier
#> description
#> <char>
#> 1: Stable OncoTree released on date 2017-11-01
#> 2: Stable OncoTree released on date 2020-10-01
#> 3: Stable OncoTree released on date 2020-02-06
#> 4: Stable OncoTree released on date 2019-12-01
#> 5: Stable OncoTree released on date 2018-07-01
#> 6: Stable OncoTree released on date 2017-06-21
#> 7: Stable OncoTree released on date 2018-08-01
#> 8: Stable OncoTree released on date 2017-10-05
#> 9: Stable OncoTree released on date 2019-08-01
#> 10: Stable OncoTree released on date 2018-09-01
#> 11: Stable OncoTree released on date 2018-06-01
#> 12: Stable OncoTree released on date 2018-03-01
#> 13: Stable OncoTree released on date 2018-04-01
#> 14: Stable OncoTree released on date 2018-05-01
#> 15: Stable OncoTree released on date 2018-02-01
#> 16: Stable OncoTree released on date 2019-05-01
#> 17: This is the closest match in TopBraid for the TumorTypes_txt file associated with release 1.1 of OncoTree (approved by committee)
#> 18: Stable OncoTree released on date 2018-01-01
#> 19: Stable OncoTree released on date 2018-06-15
#> 20: Stable OncoTree released on date 2019-02-01
#> 21: Stable OncoTree released on date 2020-04-01
#> 22: Stable OncoTree released on date 2019-03-01
#> 23: Stable OncoTree released on date 2020-02-01
#> 24: Stable OncoTree released on date 2021-11-02
#> 25: Latest OncoTree under development (subject to <b class=text-danger>change without notice</b>)
#> 26: This is the latest approved version for public use.
#> 27: Stable OncoTree released on date 2018-11-01
#> 28: 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.
#> description
#> visible release_date
#> <lgcl> <char>
#> 1: FALSE 2017-11-01
#> 2: FALSE 2020-10-01
#> 3: FALSE 2020-02-06
#> 4: FALSE 2019-12-01
#> 5: FALSE 2018-07-01
#> 6: FALSE 2017-06-21
#> 7: FALSE 2018-08-01
#> 8: FALSE 2017-10-05
#> 9: FALSE 2019-08-01
#> 10: FALSE 2018-09-01
#> 11: FALSE 2018-06-01
#> 12: FALSE 2018-03-01
#> 13: FALSE 2018-04-01
#> 14: FALSE 2018-05-01
#> 15: FALSE 2018-02-01
#> 16: FALSE 2019-05-01
#> 17: FALSE 2016-03-28
#> 18: FALSE 2018-01-01
#> 19: FALSE 2018-06-15
#> 20: FALSE 2019-02-01
#> 21: FALSE 2020-04-01
#> 22: FALSE 2019-03-01
#> 23: FALSE 2020-02-01
#> 24: FALSE 2021-11-02
#> 25: TRUE 2021-11-04
#> 26: TRUE 2021-11-02
#> 27: FALSE 2018-11-01
#> 28: TRUE 2021-11-03
#> visible release_dateMain Cancer types
The getMainCancerTypes function retrieves the main
cancer types in OncoTree.
getOncotreeMainTypes()
#> mainType
#> <char>
#> 1: Endometrial Cancer
#> 2: Melanocytoma
#> 3: Colorectal Cancer
#> 4: Peripheral Nervous System
#> 5: Uterine Sarcoma
#> ---
#> 111: Glioma
#> 112: Biliary Tract Cancer
#> 113: Prostate Cancer
#> 114: Wilms Tumor
#> 115: Renal Neuroendocrine TumorSubtypes of a specific cancer type
The getCancerSubtypes function retrieves the subtypes of
a specific cancer type.
getOncotreeTumorTypes()
#> code color name
#> <char> <char> <char>
#> 1: MMB Gray Medullomyoblastoma
#> 2: GCB LimeGreen Germinal Center B-Cell Type
#> 3: SBLU LimeGreen Splenic B-Cell Lymphoma/Leukemia, Unclassifiable
#> 4: OHNCA DarkRed Head and Neck Carcinoma, Other
#> 5: PAOS White Parosteal Osteosarcoma
#> ---
#> 881: VSC Purple Squamous Cell Carcinoma of the Vulva/Vagina
#> 882: OOVC LightBlue Ovarian Cancer, Other
#> 883: LCH LightSalmon Langerhans Cell Histiocytosis
#> 884: PSEC Green Peritoneal Serous Carcinoma
#> 885: AM LightSalmon AML with Maturation
#> mainType externalReferences tissue children
#> <char> <list> <list> <char>
#> 1: Embryonal Tumor C0205833 C3706 CNS/Brain
#> 2: Mature B-Cell Neoplasms Lymphoid
#> 3: Mature B-Cell Neoplasms Lymphoid
#> 4: Head and Neck Cancer Head and Neck
#> 5: Bone Cancer C0206642 C8969 Bone
#> ---
#> 881: Vaginal Cancer C0238518 C7736 Vulva/Vagina
#> 882: Ovarian Cancer Ovary/Fallopian Tube
#> 883: Histiocytosis C0019621 C3107 Myeloid
#> 884: Peritoneal Cancer, NOS Peritoneum
#> 885: Leukemia Myeloid
#> parent history level revocations precursors
#> <char> <list> <int> <list> <list>
#> 1: EMBT 3
#> 2: DLBCLNOS 6
#> 3: MBN 5
#> 4: HEAD_NECK 2
#> 5: OS 3
#> ---
#> 881: VULVA 2
#> 882: OVARY 2
#> 883: HDCN 4
#> 884: PERITONEUM 2
#> 885: AMLNOS 5