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_2020_04_01
#> 6: oncotree_2018_04_01
#> 7: oncotree_development
#> 8: oncotree_2019_08_01
#> 9: oncotree_2018_03_01
#> 10: oncotree_2019_05_01
#> 11: oncotree_2021_11_02
#> 12: oncotree_2020_02_06
#> 13: oncotree_candidate_release
#> 14: oncotree_2017_11_01
#> 15: oncotree_legacy_1.1
#> 16: oncotree_2019_03_01
#> 17: oncotree_2019_12_01
#> 18: oncotree_2020_10_01
#> 19: oncotree_2018_06_01
#> 20: oncotree_2018_06_15
#> 21: oncotree_latest_stable
#> 22: oncotree_2017_10_05
#> 23: oncotree_2018_05_01
#> 24: oncotree_2020_02_01
#> 25: oncotree_2018_02_01
#> 26: oncotree_2018_09_01
#> 27: oncotree_2018_01_01
#> 28: 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 2020-04-01
#> 6: Stable OncoTree released on date 2018-04-01
#> 7: Latest OncoTree under development (subject to <b class=text-danger>change without notice</b>)
#> 8: Stable OncoTree released on date 2019-08-01
#> 9: Stable OncoTree released on date 2018-03-01
#> 10: Stable OncoTree released on date 2019-05-01
#> 11: Stable OncoTree released on date 2021-11-02
#> 12: Stable OncoTree released on date 2020-02-06
#> 13: 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.
#> 14: Stable OncoTree released on date 2017-11-01
#> 15: This is the closest match in TopBraid for the TumorTypes_txt file associated with release 1.1 of OncoTree (approved by committee)
#> 16: Stable OncoTree released on date 2019-03-01
#> 17: Stable OncoTree released on date 2019-12-01
#> 18: Stable OncoTree released on date 2020-10-01
#> 19: Stable OncoTree released on date 2018-06-01
#> 20: Stable OncoTree released on date 2018-06-15
#> 21: This is the latest approved version for public use.
#> 22: Stable OncoTree released on date 2017-10-05
#> 23: Stable OncoTree released on date 2018-05-01
#> 24: Stable OncoTree released on date 2020-02-01
#> 25: Stable OncoTree released on date 2018-02-01
#> 26: Stable OncoTree released on date 2018-09-01
#> 27: Stable OncoTree released on date 2018-01-01
#> 28: 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: 2020-04-01 FALSE
#> 6: 2018-04-01 FALSE
#> 7: 2021-11-04 TRUE
#> 8: 2019-08-01 FALSE
#> 9: 2018-03-01 FALSE
#> 10: 2019-05-01 FALSE
#> 11: 2021-11-02 FALSE
#> 12: 2020-02-06 FALSE
#> 13: 2021-11-03 TRUE
#> 14: 2017-11-01 FALSE
#> 15: 2016-03-28 FALSE
#> 16: 2019-03-01 FALSE
#> 17: 2019-12-01 FALSE
#> 18: 2020-10-01 FALSE
#> 19: 2018-06-01 FALSE
#> 20: 2018-06-15 FALSE
#> 21: 2021-11-02 TRUE
#> 22: 2017-10-05 FALSE
#> 23: 2018-05-01 FALSE
#> 24: 2020-02-01 FALSE
#> 25: 2018-02-01 FALSE
#> 26: 2018-09-01 FALSE
#> 27: 2018-01-01 FALSE
#> 28: 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: 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
#> <char> <char>
#> 1: INTS LightYellow
#> 2: ISFN LimeGreen
#> 3: HPHSC DarkRed
#> 4: BRCANOS HotPink
#> 5: AMBLNOS Gray
#> ---
#> 881: SCT LightBlue
#> 882: PTCY Gray
#> 883: IMT LightYellow
#> 884: HCCIHCH MediumSeaGreen
#> 885: CEGCC Teal
#> name
#> <char>
#> 1: Intimal Sarcoma
#> 2: In Situ Follicular Neoplasia
#> 3: Hypopharynx Squamous Cell Carcinoma
#> 4: Breast Invasive Cancer, NOS
#> 5: Anaplastic Medulloblastoma, NOS
#> ---
#> 881: Steroid Cell Tumor, NOS
#> 882: Pituicytoma
#> 883: Inflammatory Myofibroblastic Tumor
#> 884: Hepatocellular Carcinoma plus Intrahepatic Cholangiocarcinoma
#> 885: Glassy Cell Carcinoma of the Cervix
#> mainType externalReferences tissue
#> <char> <list> <list>
#> 1: Soft Tissue Sarcoma C1708550 C53677
#> 2: Mature B-Cell Neoplasms [NULL] [NULL]
#> 3: Head and Neck Cancer C0280321 C4043
#> 4: Breast Cancer [NULL] [NULL]
#> 5: Large Cell/Anaplastic Medulloblastoma [NULL] [NULL]
#> ---
#> 881: Sex Cord Stromal Tumor [NULL] [NULL]
#> 882: Sellar Tumor C2986550 C94524
#> 883: Soft Tissue Sarcoma C0334121 C6481
#> 884: Hepatobiliary Cancer C0221287 C3828
#> 885: Cervical Cancer C1516407 C40212
#> children parent history level revocations precursors
#> <char> <char> <list> <int> <list> <list>
#> 1: Soft Tissue SOFT_TISSUE 2
#> 2: Lymphoid FL 6
#> 3: Head and Neck HNSC 3
#> 4: Breast BRCA 3
#> 5: CNS/Brain AMBL 4
#> ---
#> 881: Ovary/Fallopian Tube SCST 3
#> 882: CNS/Brain SELT 3
#> 883: Soft Tissue SOFT_TISSUE 2
#> 884: Liver LIVER 2
#> 885: Cervix CERVIX 2