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_2018_11_01
#> 2: oncotree_2017_06_21
#> 3: oncotree_2018_07_01
#> 4: oncotree_2019_02_01
#> 5: oncotree_2025_10_03
#> 6: oncotree_2020_04_01
#> 7: oncotree_2018_04_01
#> 8: oncotree_development
#> 9: oncotree_2019_08_01
#> 10: oncotree_2025_04_08
#> 11: oncotree_2018_03_01
#> 12: oncotree_2019_05_01
#> 13: oncotree_2021_11_02
#> 14: oncotree_2020_02_06
#> 15: oncotree_candidate_release
#> 16: oncotree_2017_11_01
#> 17: oncotree_legacy_1.1
#> 18: oncotree_2019_03_01
#> 19: oncotree_2019_12_01
#> 20: oncotree_2020_10_01
#> 21: oncotree_2018_06_01
#> 22: oncotree_2018_06_15
#> 23: oncotree_latest_stable
#> 24: oncotree_2017_10_05
#> 25: oncotree_2018_05_01
#> 26: oncotree_2020_02_01
#> 27: oncotree_2018_02_01
#> 28: oncotree_2018_09_01
#> 29: oncotree_2018_01_01
#> 30: oncotree_2018_08_01
#> api_identifier
#> description
#> <char>
#> 1: Stable OncoTree released on date 2018-11-01
#> 2: Stable OncoTree released on date 2017-06-21
#> 3: Stable OncoTree released on date 2018-07-01
#> 4: Stable OncoTree released on date 2019-02-01
#> 5: Stable OncoTree released on date 2025-10-03
#> 6: Stable OncoTree released on date 2020-04-01
#> 7: Stable OncoTree released on date 2018-04-01
#> 8: Latest OncoTree under development (subject to <b class=text-danger>change without notice</b>)
#> 9: Stable OncoTree released on date 2019-08-01
#> 10: Stable OncoTree released on date 2025-04-08
#> 11: Stable OncoTree released on date 2018-03-01
#> 12: Stable OncoTree released on date 2019-05-01
#> 13: Stable OncoTree released on date 2021-11-02
#> 14: Stable OncoTree released on date 2020-02-06
#> 15: 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.
#> 16: Stable OncoTree released on date 2017-11-01
#> 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 2019-03-01
#> 19: Stable OncoTree released on date 2019-12-01
#> 20: Stable OncoTree released on date 2020-10-01
#> 21: Stable OncoTree released on date 2018-06-01
#> 22: Stable OncoTree released on date 2018-06-15
#> 23: This is the latest approved version for public use.
#> 24: Stable OncoTree released on date 2017-10-05
#> 25: Stable OncoTree released on date 2018-05-01
#> 26: Stable OncoTree released on date 2020-02-01
#> 27: Stable OncoTree released on date 2018-02-01
#> 28: Stable OncoTree released on date 2018-09-01
#> 29: Stable OncoTree released on date 2018-01-01
#> 30: Stable OncoTree released on date 2018-08-01
#> description
#> release_date visible
#> <char> <lgcl>
#> 1: 2018-11-01 FALSE
#> 2: 2017-06-21 FALSE
#> 3: 2018-07-01 FALSE
#> 4: 2019-02-01 FALSE
#> 5: 2025-10-03 FALSE
#> 6: 2020-04-01 FALSE
#> 7: 2018-04-01 FALSE
#> 8: 2021-11-04 TRUE
#> 9: 2019-08-01 FALSE
#> 10: 2025-04-08 FALSE
#> 11: 2018-03-01 FALSE
#> 12: 2019-05-01 FALSE
#> 13: 2021-11-02 FALSE
#> 14: 2020-02-06 FALSE
#> 15: 2021-11-03 TRUE
#> 16: 2017-11-01 FALSE
#> 17: 2016-03-28 FALSE
#> 18: 2019-03-01 FALSE
#> 19: 2019-12-01 FALSE
#> 20: 2020-10-01 FALSE
#> 21: 2018-06-01 FALSE
#> 22: 2018-06-15 FALSE
#> 23: 2025-10-03 TRUE
#> 24: 2017-10-05 FALSE
#> 25: 2018-05-01 FALSE
#> 26: 2020-02-01 FALSE
#> 27: 2018-02-01 FALSE
#> 28: 2018-09-01 FALSE
#> 29: 2018-01-01 FALSE
#> 30: 2018-08-01 FALSE
#> release_date visibleMain Cancer types
The getMainCancerTypes function retrieves the main
cancer types in OncoTree.
getOncotreeMainTypes()
#> mainType
#> <char>
#> 1: Endometrial Cancer
#> 2: Neoplastic Vs Reactive
#> 3: Melanocytoma
#> 4: Colorectal Cancer
#> 5: Peripheral Nervous System
#> ---
#> 116: Glioma
#> 117: Biliary Tract Cancer
#> 118: Prostate Cancer
#> 119: Wilms Tumor
#> 120: Renal Neuroendocrine TumorSubtypes of a specific cancer type
The getCancerSubtypes function retrieves the subtypes of
a specific cancer type.
getOncotreeTumorTypes()
#> code color
#> <char> <char>
#> 1: ASM LightSalmon
#> 2: INTS LightYellow
#> 3: HPHSC DarkRed
#> 4: TAML LightSalmon
#> 5: BRCANOS HotPink
#> ---
#> 894: ASTR4 Gray
#> 895: PTCY Gray
#> 896: IMT LightYellow
#> 897: HCCIHCH MediumSeaGreen
#> 898: CEGCC Teal
#> name
#> <char>
#> 1: Aggressive Systemic Mastocytosis
#> 2: Intimal Sarcoma
#> 3: Hypopharynx Squamous Cell Carcinoma
#> 4: Therapy-Related Acute Myeloid Leukemia
#> 5: Breast Invasive Cancer, NOS
#> ---
#> 894: Astrocytoma, IDH-Mutant, Grade 4
#> 895: Pituicytoma
#> 896: Inflammatory Myofibroblastic Tumor
#> 897: Hepatocellular Carcinoma plus Intrahepatic Cholangiocarcinoma
#> 898: Glassy Cell Carcinoma of the Cervix
#> mainType externalReferences
#> <char> <list>
#> 1: Mastocytosis C1112486
#> 2: Soft Tissue Sarcoma C1708550
#> 3: Head and Neck Cancer C0280321
#> 4: Leukemia C1336735
#> 5: Breast Cancer [NULL]
#> ---
#> 894: Gliomas, Glioneuronal Tumors, and Neuronal Tumors [NULL]
#> 895: Sellar Tumor C2986550
#> 896: Soft Tissue Sarcoma C0334121
#> 897: Hepatobiliary Cancer C0221287
#> 898: Cervical Cancer C1516407
#> tissue children parent history level revocations precursors
#> <list> <char> <char> <list> <int> <list> <list>
#> 1: C9285 Myeloid SM 5
#> 2: C53677 Soft Tissue SOFT_TISSUE 2
#> 3: C4043 Head and Neck HNSC 3
#> 4: C8252 Myeloid TMN 5
#> 5: [NULL] Breast BRCA 3
#> ---
#> 894: [NULL] CNS/Brain ASTR 5
#> 895: C94524 CNS/Brain SELT 3
#> 896: C6481 Soft Tissue SOFT_TISSUE 2
#> 897: C3828 Liver LIVER 2
#> 898: C40212 Cervix CERVIX 2