OncoTree is a comprehensive, community-led cancer classification system that adapts to the evolving demands of precision oncology. Designed to classify cancers by both histological and molecular traits, it provides a structured framework to complement the clinical decision-making processes. The platform, which is open-source and publicly accessible, is governed by a diverse committee of oncologists, pathologists, and scientists. This multidisciplinary oversight ensures OncoTree remains relevant, incorporating new cancer types and research advancements in real time to support clinical decision-making and research applications.
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OncoTree is a comprehensive, community-led cancer classification system that adapts to the evolving demands of precision oncology. Designed to classify cancers by both histological and molecular traits, it provides a structured framework to complement the clinical decision-making processes. The platform, which is open-source and publicly accessible, is governed by a diverse committee of oncologists, pathologists, and scientists. This multidisciplinary oversight ensures OncoTree remains relevant, incorporating new cancer types and research advancements in real time to support clinical decision-making and research applications.
The OncoTree Mapping tool was developed to facilitate the mapping of OncoTree codes between different OncoTree release versions. Below you can find basic instructions in the "Running the tool" section, and a detailed walkthrough in the "Tutorial" section.
As of January 2020, the sun has set on Python 2.X. If you are still using Python 2.X, we encourage you to use Python 3.6 and above, but here is the last version of the code to work with Python 2.X. In the future, only Python 3.X versions of this tool will be supported.
-i | --source-file: This is the source clinical file path. It must contain ONCOTREE_CODE in the file header and it must contain OncoTree codes corresponding to the <source_oncotree_version>. Read more about the cBioPortal clinical file format here.
-o | --target-file: This is the path to the target clinical file that will be generated. It will contain mapped OncoTree codes from <source_oncotree_version>-to-<target_oncotree_version>.
-s | --source-version: This is the source OncoTree version. The OncoTree codes in the source file must correspond to this version.
-t | --target-version: This is the target OncoTree version that the script will attempt to map the source file OncoTree codes to.
The list of OncoTree versions available are viewable here or on the dropdown menu of the OncoTree home page.
Note: the source file should not contain embedded line breaks within any single cell in the table, such as those created by using the keyboard combinations Alt-Enter or Command-Option-Enter while editing a cell in Microsoft Excel.
For a detailed walkthrough of running the tool, see the "Tutorial" section below.
The OncoTree Mapper Tool will automatically replace the value in the ONCOTREE_CODE column with the mapped code if available. The tool will also add a new column called ONCOTREE_CODE_OPTIONS containing suggestions for OncoTree codes if one or more nodes could not be directly mapped. The ONCOTREE_CODE_OPTIONS column formats its suggestions differently depending on the mapping results. Possible suggestion formats and corresponding examples are shown below.
Unambiguous direct mappings occur when an OncoTree code maps directly to a single code in the target version. In this case, the ONCOTREE_CODE_OPTIONS column will be left blank, and the mapped code will be automatically placed in the ONCOTREE_CODE column. Unambiguous direct mappings are checked for addition of more granular nodes; to see how this may affect the ONCOTREE_CODE_OPTIONS column formatting, please refer to the subsection below "4. More Granular Nodes Introduced".
Ambiguous direct mappings occur when an OncoTree code maps to multiple codes in the target version. The ONCOTREE_CODE_OPTIONS column formats the output as follows:
'Source Code' -> {'Code 1', 'Code 2', 'Code 3', } e.g. ALL -> {TLL, BLL}
Example: Schema describing the revocation of OncoTree node ALL is mapped to multiple nodes.
In oncotree_2018_05_01, ALL had two children: TALL and BALL. On release oncotree_2018_06_01, the ALL node was discontinued and the TALL node was renamed TLL and the BALL node was renamed BLL.
The ONCOTREE_CODE_OPTIONS column would be shown as follows:
ALL -> {TLL, BLL}
Ambiguous direct mappings are also checked for addition of more granular nodes; to see how this may affect the ONCOTREE_CODE_OPTIONS column formatting, please refer to the subsection below "4. More Granular Nodes Introduced".
No direct mappings occur when the source OncoTree code is unrelated to any OncoTree code in the target version. One such possibility is mapping a newly introduced OncoTree code backwards in time. In this case, the tool finds the closest set of neighbors (e.g parents and children) which are mappable in the target version. The ONCOTREE_CODE_OPTIONS column returns the set with the keyword Neighbors as follows:
Example: Schema describing a case where new OncoTree node UPA cannot be directly mapped backwards to a node.
In oncotree_2019_03_01, UPA was added to the OncoTree as a child node of BLADDER. Because UPA did not exist in previous version oncotree_2018_05_01 and did not replace any existing node, the tool uses the surrounding nodes when mapping backwards. In this case, the parent node BLADDER is returned as the closest match.
The ONCOTREE_CODE_OPTIONS column would be shown as follows:
In certain cases, the target version can also introduce nodes with more specific descriptions. When this occurs, the tool will add the string more granular choices introduced to the existing text in the ONCOTREE_CODE_OPTIONS column as follows:
'Source Code' -> {'Code 1', }, more granular choices introduced e.g. TALL -> {TLL}, more granular choices introduced
Example: Schema describing a case where OncoTree node TALL is mapped to a node with more granular children
In oncotree_2019_03_01, TALL was a leaf node with no children. In release oncotree_2019_06_01, TLL was introduced as a replacement for TALL with additional children ETPLL and NKCLL.
The ONCOTREE_CODE_OPTIONS column would be shown as follows:
An invalid source OncoTree Code means the provided code cannot be found in the source version. In such a case, mapping cannot be attempted and the ONCOTREE_CODE_OPTIONS column displays the following:
'Source Code' -> ???, OncoTree code not in source OncoTree version
The following tutorial will guide the user through using the oncotree_to_oncotree.py tool. The tutorial will go through the expected output to highlight specific mapping cases. Additionally, the tutorial will cross-reference the output with the generated mapping summary to demonstrate how it can be used to aid in manual selection of unresolved nodes.
The tool will output two files: data_clinical_sample_remapped.txt and data_clinical_sample_remapped_summary.html. For your reference, you can see the expected output files - here and here
Using values in the ONCOTREE_CODE_OPTIONS as a guide, manually select and place an OncoTree Code in the ONCOTREE_CODE column. For additional information, refer to the summary file data_clinical_sample_remapped_summary.html. Repeat for all rows in the output file. Several examples are shown below.
ALL -> {BLL,TLL}, more granular choices introduced
Source OncoTree code ALL maps directly to codes BLL and TLL. Users should place either BLL or TLL in the ONCOTREE_CODE column. The ONCOTREE_CODE_OPTIONS column also notes that more granular choices were introduced; as such, users can use the summary file for additional guidance.
Searching by source code, the following information can be found in the summary file:
The summary file provides a link to the closest shared parent node LNM; users can choose more granular nodes by referencing the provided tree:
Source OncoTree code BALL maps directly to BLL. Users should place BLL in the ONCOTREE_CODE column. However, similar to sample 1, the ONCOTREE_CODE_OPTIONS indicates there are more granular choices available. Users can follow the same steps as above and use the summary file to select a more granular node.
No additional resolution is needed; the previous OncoTree code was already automatically mapped to PTCL and placed in the ONCOTREE_CODE column. ONCOTREE_CODE_OPTIONS is empty because no manual selections were necessary.
HGNEE -> ???, OncoTree code not in source OncoTree version
Source OncoTree code HGNEE was not found in the source OncoTree version and therefore could not be mapped. Users can either reassign a new source OncoTree code (and rerun the script) or remove the sample.
After filling in the ONCOTREE_CODE column with an OncoTree code for each sample, use an editor (e.g. Microsoft Excel, vim, etc.) to trim off the ONCOTREE_CODE_OPTIONS column. The resulting file will be a new data_clinical_sample.txt file with all codes mapped to the target version. The first four columns of the final result is shown below:
The Ontology Mapping tool was developed to facilitate the mapping between different cancer classification systems. We currently support mapping between OncoTree, ICD-O, NCIt, UMLS and HemeOnc systems. The tool and the mapping file (the mapping file does not need to be downloaded to run the tool) can be found here
i | --source-file: This is the source file path. The source file must contain one of the ONCOTREE_CODE, NCIT_CODE, UMLS_CODE, ICDO_TOPOGRAPHY_CODE, ICDO_MORPHOLOGY_CODE or HEMEONC_CODE in the file header and it must contain codes corresponding to the Ontology System.
o | --target-file: This is the path to the target file that will be generated. It will contain ontologies mapped from source code in <source-file> to <target-code>.
s | --source-code: This is the source ontology code in <source-file>. It must be one of the ONCOTREE_CODE, NCIT_CODE, UMLS_CODE, ICDO_TOPOGRAPHY_CODE, ICDO_MORPHOLOGY_CODE or HEMEONC_CODE.
t | --target-code: This is the target ontology code that the script will attempt to map the source file ontology code to. It must be one of the ONCOTREE_CODE, NCIT_CODE, UMLS_CODE, ICDO_TOPOGRAPHY_CODE, ICDO_MORPHOLOGY_CODE or HEMEONC_CODE.
Note
The source file should be tab delimited and should contain one of the ontology: ONCOTREE_CODE, NCIT_CODE, UMLS_CODE, ICDO_TOPOGRAPHY_CODE, ICDO_MORPHOLOGY_CODE or HEMEONC_CODE in the file header.
We currently are allowing only one ontology to another ontology mapping. In the future, we plan to extend the tool to support mapping to multiple ontology systems.
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+import{_ as e,c as t,o,a3 as a}from"./chunks/framework.CyEiTwkJ.js";const m=JSON.parse('{"title":"Contents","description":"","frontmatter":{},"headers":[],"relativePath":"mapping.md","filePath":"mapping.md"}'),d={name:"mapping.md"},n=a("",88),r=[n];function c(i,l,s,h,p,u){return o(),t("div",null,r)}const O=e(d,[["render",c]]);export{m as __pageData,O as default};
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+import{_ as l,c as i,o as r,a3 as a,j as e,a as o}from"./chunks/framework.CyEiTwkJ.js";const y=JSON.parse('{"title":"News","description":"","frontmatter":{},"headers":[],"relativePath":"news.md","filePath":"news.md"}'),t={name:"news.md"},n=a('
New Stable Release OncoTree version oncotree_2021_11_02 is now the latest stable release. The previous stable version is still accessible as version oncotree_2020_10_01.
New nodes added:
Desmoplastic/Nodular Medulloblastoma, NOS (DMBLNOS)
Medulloblastoma with Extensive Nodularity, NOS (MBENNOS)
Medulloblastoma with Extensive Nodularity, SHH Subtype (MBENSHH)
Pancreatic Neuroendocrine Carcinoma (PANEC) in the original version of this news release this node was accidentally omitted
Nodes reclassified
The following list of oncotree codes had the mainType shortened to drop the suffix "NOS": ADRENAL_GLAND, AMPULLA_OF_VATER, BILIARY_TRACT, BLADDER, BONE, BOWEL, BRAIN, BREAST, CERVIX, EYE, HEAD_NECK, KIDNEY, LIVER, LUNG, LYMPH, MYELOID, OTHER, OVARY, PANCREAS, PENIS, PERITONEUM, PLEURA, PNS, PROSTATE, SKIN, SOFT_TISSUE, STOMACH, TESTIS, THYMUS, THYROID, UTERUS, VULVA
Cholangiocarcinoma (CHOL) now has direct parent Intraductal Papillary Neoplasm of the Bile Duct (IPN) [previously: Biliary Tract (BILIARY_TRACT)]
Gallbladder Cancer (GBC) now has direct parent Intracholecystic Papillary Neoplasm (ICPN) [previously: Biliary Tract (BILIARY_TRACT)]
oncotree candidate release version additions:
Three new nodes intended only for version oncotree_candidate_release were added (NVRINT, MPNWP, MDSWP). These nodes will not be incorperated into oncotree latest stable.
resources added
rdf formatted OWL ontology and taxomomy files for recent oncotree versions have been added to our github repository. They can be explored here .
The Ontology Mapping tool was developed to facilitate the mapping between different cancer classification systems. We currently support mapping between OncoTree, ICD-O, NCIt, UMLS and HemeOnc systems.
A mapping file containing mappings between the different ontologies and OncoTree codes as well as a python script to run the mapping is available on the OncoTree GitHub page . Details are also available on the Mapping Tools page .
The mapping file is expected to grow as we curate more ontology mappings for OncoTree codes.
New Stable Release OncoTree version oncotree_2020_10_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2020_04_01.
New nodes added:
Basal Cell Carcinoma of Prostate (BCCP)
Node deleted:
Porphyria Cutania Tarda (PCT)
Node with updated name:
Goblet Cell Adenocarcinoma of the Appendix (GCCAP) [previously: Goblet Cell Carcinoid of the Appendix (GCCAP)].
New Stable Release OncoTree version oncotree_2020_04_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2020_02_06.
New nodes added:
AML with Variant RARA translocation (AMLRARA)
Nodes reclassified:
Mixed Cancer Types (MIXED is now a child of Other (OTHER) [previously under: Cancer of Unknown Primary (CUP)].
When providing web links to oncotree, you may include a search term as an optional argument and the oncotree you reference will be displayed with the search term located and highlighted. Use of this mechanism can be seen in the example output for the OncoTree-to-OncoTree code mapping tool.
As an example, you can provide a direct link to the TumorType node PANET in oncotree version oncotree_2019_12_01 with this link: http://oncotree.mskcc.org/#/home?version=oncotree_2019_12_01&search_term=(PANET)
New Stable Release OncoTree version oncotree_2020_02_06 is now the latest stable release. The previous stable version is still accessible as version oncotree_2020_02_01.
Nodes reclassified:
Gallbladder Cancer (GBC) is now a child of Biliary Tract (BILIARY_TRACT) [previously under: Intracholecystic Papillary Neoplasm (ICPN)].
Cholangiocarcinoma (CHOL) is now a child of Biliary Tract (BILIARY_TRACT) [previously under: Intraductal Papillary Neoplasm of the Bile Duct (IPN)].
New Stable Release OncoTree version oncotree_2020_02_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2019_12_01.
New nodes added:
Intraductal Oncocytic Papillary Neoplasm (IOPN)
Intraductal Tubulopapillary Neoplasm (ITPN)
Intracholecystic Papillary Neoplasm (ICPN)
Intraductal Papillary Neoplasm of the Bile Duct (IPN)
Nodes reclassified:
Gallbladder Cancer (GBC) is now a child of Intracholecystic Papillary Neoplasm (ICPN) [previously under: Biliary Tract (BILIARY_TRACT)].
Cholangiocarcinoma (CHOL) is now a child of Intraductal Papillary Neoplasm of the Bile Duct (IPN) [previously under: Biliary Tract (BILIARY_TRACT)].
New Stable Release OncoTree version oncotree_2019_12_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2019_08_01.
New Stable Release OncoTree version oncotree_2019_08_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2019_05_01.
New nodes added:
Lacrimal Gland Tumor (LGT)
Adenoid Cystic Carcinoma of the Lacrimal Gland (ACLG)
Squamous Cell Carcinoma of the Lacrimal Gland (SCLG)
New Stable Release OncoTree version oncotree_2019_05_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2019_03_01.
Nodes reclassified
Intestinal Ampullary Carcinoma (IAMPCA) MainType is now Ampullary Cancer [previously: Ampullary Carcinoma]
Mixed Ampullary Carcinoma (MAMPCA) MainType is now Ampullary Cancer [previously: Ampullary Carcinoma]
Pancreatobiliary Ampullary Carcinoma (PAMPCA) MainType is now Ampullary Cancer [previously: Ampullary Carcinoma]
Ependymoma (EPM) MainType is now Glioma [previously: CNS Cancer]
Rosai-Dorfman Disease (RDD) MainType is now Histiocytosis [previously: Histiocytic Disorder]
The OncoTree-to-OncoTree mapping tool (now version 1.1) has been slightly improved, mainly by adding a separate section in the output summary for reporting OncoTree codes which were replaced automatically. Also, additional documentation and description of the tool has been added under the "Mapping Tools" tab.
A python program is now available for download under the webpage tab labeled "Mapping Tools". This tool will rewrite OncoTree codes in a tabular clinical data file, mapping from one version of OncoTree to another. When additional guidance is necessary, the program will insert a column containing options and comments next to the ONCOTREE_CODE column. After selecting an appropriate OncoTree code for cases which require action, this extra column can be deleted to produce a fully re-mapped clinical data file. More details about this tool and how to use it are available under the "Mapping Tools" tab.
The OncoTree-to-OncoTree mapping tool relies on an expanded model of OncoTree node history. This is reflected in the Web API schema for Tumor Types, which now has added properties called "precursors" and "revocations". Using these properties, and the existing "history" property, the tool is able to make proper mappings across OncoTree versions, and give suggestions when no clear mapping is available. It is also reflected in the main tree visualization of OncoTree, where a combination of these properties (when set) will be displayed in the pop-up information box with label "Previous Codes".
New Stable Release OncoTree version oncotree_2019_03_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2019_02_01.
Development of a tool to map OncoTree codes between different versions of OncoTree is nearing completion.
Related to this, users of the OncoTree Web API should be aware that we will soon be adding two additional properties to the output schema returned by the api/tumorTypes endpoints. The properties "precursors" and "revocations" will be added alongside the "history" property (having the same type: an array of strings). These will help distinguish the kinds of possible relationships to OncoTree nodes in prior versions of OncoTree. We expect this new schema to be backwards compatible, but if your language or tools requires an exactly matching JSON schema you will need to make adjustments.
New Stable Release OncoTree version oncotree_2019_02_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2018_11_01.
New Stable Release OncoTree version oncotree_2018_11_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2018_09_01.
New nodes added:
Gastrointestinal Neuroendocrine Tumors of the Esophagus/Stomach (GINETES)
High-Grade Neuroendocrine Carcinoma of the Esophagus (HGNEE)
High-Grade Neuroendocrine Carcinoma of the Stomach (HGNES)
Nodes reclassified:
Well-Differentiated Neuroendocrine Tumors of the Stomach (SWDNET) is now a child of Gastrointestinal Neuroendocrine Tumors of the Esophagus/Stomach (GINETES) [previously under: Bowel (BOWEL)].
New Stable Release OncoTree version oncotree_2018_09_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2018_08_01.
New Stable Release OncoTree version oncotree_2018_08_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2018_07_01.
New nodes added:
Angiomatoid Fibrous Histiocytoma (AFH)
Clear Cell Sarcoma of Kidney (CCSK)
Ewing Sarcoma of Soft Tissue (ESST)
Extra Gonadal Germ Cell Tumor (EGCT)
Infantile Fibrosarcoma (IFS)
Malignant Glomus Tumor (MGST)
Malignant Rhabdoid Tumor of the Liver (MRTL)
Myofibromatosis (IMS)
Sialoblastoma (SBL)
Undifferentiated Embryonal Sarcoma of the Liver (UESL)
New Stable Release OncoTree version oncotree_2018_07_01 is now the latest stable release. The previous stable version is still accessible through the OncoTree web API by requesting version oncotree_2018_06_15.
New Stable Release OncoTree version oncotree_2018_06_15 is now the latest stable release. The previous stable version is still accessible through the OncoTree web API by requesting version oncotree_2018_06_01.
Nodes reclassified
Mature B-Cell Neoplasms (MBN) and Mature T and NK Neoplasms (MTNN) and their subnodes were relocated to be under Non-Hodgkin Lymphoma (NHL).
Rosai-Dorfman Disease (RDD) was relocated to be under Histiocytic and Dendritic Cell Neoplasms (HDCN). Previously RDD was under Lymphoid Neoplasm (LNM) in the Lymphoid category.
New Stable Release OncoTree version oncotree_2018_06_01 is now the latest stable release. The previous stable version is still accessible through the OncoTree web API by requesting version oncotree_2018_05_01.
Blood and Lymph subtrees replaced with new Myeloid and Lymphoid subtrees:
23 nodes in the previous Blood subtree have been deleted or relocated/renamed. Affected OncoTree codes from this tree: BLOOD, BPDCN, HIST, LCH, ECD, LEUK, ALL, BALL, TALL, AMOL, AML, CLL, CML, CMML, HCL, LGLL, MM, MDS, MPN, ETC, MYF, PCV, SM
28 nodes in the previous Lymph subtree have been deleted or relocated/renamed. Affected OncoTree codes from this tree: LYMPH, HL, CHL, NLPHL, NHL, BCL, BL, DLBCL, MALTL, FL, MCL, MZL, MBCL, NMZL, PCNSL, PEL, SLL, SMZL, WM, TNKL, CTCL, MYCF, SEZS, PTCL, ALCL, AITL, PTCLNOS, RD
101 nodes in the current Myeloid subtree have been added or relocated/renamed from previous subtrees. OncoTree codes in this new subtree are: MYELOID, MATPL, MBGN, MNM, ALAL, AUL, MPALBCRABL1, MPALKMT2A, MPALBNOS, MPALTNOS, AML, AMLMRC, AMLRGA, AMLRBM15MKL1, AMLBCRABL1, AMLCEBPA, AMLNPM1, AMLRUNX1, AMLCBFBMYH11, AMLGATA2MECOM, AMLDEKNUP214, AMLRUNX1RUNX1T1, AMLMLLT3KMT2A, APLPMLRARA, AMLNOS, AM, AMLMD, AWM, ABL, AMKL, AMOL, AMML, APMF, PERL, MPRDS, MLADS, TAM, MS, TMN, TAML, TMDS, BPDCN, HDCN, JXG, ECD, FRCT, FDCS, HS, IDCT, IDCS, LCH, LCS, MCD, CMCD, MCSL, SM, ASM, ISM, SMMCL, SSM, SMAHN, MDS, MDSEB, MDSEB1, MDSEB2, MDSID5Q, MDSMD, MDSRS, MDSRSMD, MDSRSSLD, MDSSLD, MDSU, RCYC, MDS/MPN, aCML, CMML, CMML0, CMML1, CMML2, JMML, MDSMPNRST, MDSMPNU, MNGLP, MLNER, MLNFGFR1, MLNPCM1JAK2, MLNPDGFRA, MLNPDGFRB, MPN, CELNOS, CML, CMLBCRABL1, CNL, ET, ETMF, MPNU, PV, PVMF, PMF, PMFPES, PMFOFS
Nodes reclassified
Adrenocortical Adenoma (ACA) MainType is now Adrenocortical Adenoma [previously: Adrenocortical Carcinoma]
Ampulla of Vater (AMPULLA_OF_VATER) MainType is now Ampullary Cancer [previously: Ampullary Carcinoma]
Parathyroid Cancer (PTH) MainType is now Parathyroid Cancer [previously: Head and Neck Cancer]
Parathyroid Carcinoma (PTHC) MainType is now Parathyroid Cancer [previously: Head and Neck Cancer]
Follicular Dendritic Cell Sarcoma (FDCS) was moved from the Soft Tissue subtree into the Myeloid subtree with direct parent Histiocytic and Dendritic Cell Neoplasms (HDCN)
Interdigitating Dendritic Cell Sarcoma (IDCS) was moved from the Soft Tissue subtree into the Myeloid subtree with direct parent Histiocytic and Dendritic Cell Neoplasms (HDCN)
New nodes added:
Inverted Urothelial Papilloma (IUP)
Urothelial Papilloma (UPA)
Oncocytic Adenoma of the Thyroid (OAT)
Character set simplification
Salivary Gland-Type Tumor of the Lung (SGTTL) used to contain a unicode character for a horizontal dash. This punctuation mark is now a hyphen.
New Stable Release OncoTree version oncotree_2018_05_01 is now the latest stable release. The previous stable version is still accessible through the OncoTree web API by requesting version oncotree_2018_04_01.
New nodes added:
Primary CNS Melanocytic Tumors (PCNSMT)
Melanocytoma (MELC)
Node reclassified
Primary CNS Melanoma (PCNSM) now is a child of Primary CNS Melanocytic Tumors (PCNSMT) [previously under: CNS/Brain].
',44),s=e("ul",null,[e("li",null,[e("strong",null,"New Web API Version Available"),e("ul",null,[e("li",null,[o("A new version (v1.0.0) of the OncoTree Web API is available. It can be explored here: "),e("a",{href:"http://oncotree.mskcc.org/swagger-ui.html",target:"_blank",rel:"noreferrer"},"http://oncotree.mskcc.org/swagger-ui.html"),o(),e("br"),o(" The previous version is still available, but is scheduled to be discontinued May 31, 2018 You can continue to access the previous version (v0.0.1) in its original location summarized here: ~~"),e("a",{href:"http://oncotree.mskcc.org/oncotree/swagger-ui.html~~",target:"_blank",rel:"noreferrer"},"http://oncotree.mskcc.org/oncotree/swagger-ui.html~~")])])]),e("li",null,[e("strong",null,"Details and Migration Guidance"),e("ul",null,[e("li",null,[o("The base URL for accessing all API functionality is being simplified from ~~"),e("a",{href:"http://oncotree.mskcc.org/oncotree/~~",target:"_blank",rel:"noreferrer"},"http://oncotree.mskcc.org/oncotree/~~"),o(" to "),e("a",{href:"http://oncotree.mskcc.org/",target:"_blank",rel:"noreferrer"},"http://oncotree.mskcc.org/")]),e("li",null,[e("span",{class:"oi oi-warning text-danger","aria-hidden":"true"}),o(" The /api/tumor_types.txt endpoint is now deprecated. It is scheduled for deletion as part of the next API version release.")]),e("li",null,[o("Most endpoint paths in the API remain the same and provide the same services. Exceptions are: "),e("ul",null,[e("li",null,'/api/tumorTypes used to accept a query parameter ("flat") which controlled the output format for receiving a tree representation or a flat representation of the full set of TumorTypes. Now this endpoint always returns a flat list of all TumorTypes and a new endpoint path (/api/tumorTypes/tree) is used to retrieve a tree representation of the OncoTree. Previous requests which included "flat=false" should be adjusted to use the /api/tumorTypes/tree endpoint. Otherwise "flat=true" should be dropped from the request.'),e("li",null,'/api/tumorTypes used to accept a query parameter ("deprecated") which is no longer recognized. This parameter should be dropped from requests. Deprecated OncoTree codes can instead be found in the history attribute of the response.'),e("li",null,"the POST request endpoint (/api/tumorTypes/search) which accepted a list of TumorType queries has been deprecated and is no longer available through the swagger-ui interface. The GET request endpoint /api/tumorTypes/search/{type}/{query} remains available as before. If you previously submitted an array of query requests, you should iterate through the array and call the GET request endpoint to make one query per request.")])]),e("li",null,[o("The output format (schema) of many endpoints has been simplified. You will need to adjust your result handling accordingly. Changes include: "),e("ul",null,[e("li",null,'responses no longer include a "meta" element with associated code and error messages. Instead HTTP status codes are set appropriately and error messages are supplied in message bodies. Responses also no longer contain a "data" element. Objects representing the API output are directly returned instead.'),e("li",null,"MainType values are no longer modeled as objects. Each MainType value is now represented as a simple string. The /api/mainTypes endpoint now returns an array of strings rather than an object mapping MainType names to MainType objects."),e("li",{"UMLS:":"","[CL497188,C1510796],NCI:":"","[C123384,C40361]":""},'TumorType values no longer contain elements "id", "deprecated", "links", "NCI", "UMLS". A new element ("externalReferences") has been added which contains a JSON object mapping external authority names to arrays of associated identifiers. Such as "externalReferences":')])]),e("li",null,'Argument validation has been strengthened for several parameters, such as "type" and "levels" in the /api/tumorTypes/search/{type}/{query} endpoint. Now improper arguments cause an a HTTP status response indicating error, with a description of the problem in the body.'),e("li",null,[o("Some requests which fail to find matching entities now return NOT_FOUND HTTP status code 404 rather than an empty result. Examples: "),e("a",{href:"http://oncotree.mskcc.org/api/tumorTypes/search/code/TEST_UNDEFINED_CODE",target:"_blank",rel:"noreferrer"},"http://oncotree.mskcc.org/api/tumorTypes/search/code/TEST_UNDEFINED_CODE"),o(" or "),e("a",{href:"http://oncotree.mskcc.org/api/crosswalk?vocabularyId=ICDO&conceptId=C15",target:"_blank",rel:"noreferrer"},"http://oncotree.mskcc.org/api/crosswalk?vocabularyId=ICDO&conceptId=C15")])])])],-1),c=a('
New Stable Release OncoTree version oncotree_2018_04_01 is now the latest stable release. The previous stable version is still accessible through the OncoTree web API by requesting version oncotree_2018_03_01.
New Stable Release OncoTree version oncotree_2018_03_01 is now the latest stable release. The previous stable version is still accessible through the OncoTree web API by requesting version oncotree_2018_02_01.
New node added:
Ganglioneuroma (GN)
Node reclassified
Rhabdoid Cancer (MRT) now has direct parent Kidney (KIDNEY) [previously: Wilms' Tumor (WT)] Main type is now "Rhabdoid Cancer" [previously: Wilms Tumor]
OncoTree format expanded to support deeper tree nodes
To support upcoming expansion of the OncoTree, the 5 named levels of the OncoTree {Primary, Secondary, Tertiary, Quaternary, Quinternary} have been dropped in favor of level numbers {1, 2, 3, 4, 5, ...}. Web API functions have been adjusted accordingly, and an API function which outputs a table format of the OncoTree has been adjusted to output 7 levels of depth.
New Stable Release OncoTree version oncotree_2018_02_01 is now the latest stable release. The previous stable version is still accessible for use through version name oncotree_2018_01_01.
New nodes added:
Adenosquamous Carcinoma of the Gallbladder (GBASC)
Gallbladder Adenocarcinoma, NOS (GBAD)
Small Cell Gallbladder Carcinoma (SCGBC)
Juvenile Secretory Carcinoma of the Breast (JSCB)
Osteoclastic Giant Cell Tumor (OSGCT)
Peritoneal Serous Carcinoma (PSEC)
Nodes reclassified [from: Embryonal Tumor, to: Peripheral Nervous System]:
Ganglioneuroblastoma (GNBL)
Neuroblastoma (NBL)
Node with renamed OncoTree code:
Spindle Cell Carcinoma of the Lung (SPCC) [previously: SpCC]
The OncoTree Mapping tool was developed to facilitate the mapping of OncoTree codes between different OncoTree release versions. Below you can find basic instructions in the "Running the tool" section, and a detailed walkthrough in the "Tutorial" section.
As of January 2020, the sun has set on Python 2.X. If you are still using Python 2.X, we encourage you to use Python 3.6 and above, but here is the last version of the code to work with Python 2.X. In the future, only Python 3.X versions of this tool will be supported.
-i | --source-file: This is the source clinical file path. It must contain ONCOTREE_CODE in the file header and it must contain OncoTree codes corresponding to the <source_oncotree_version>. Read more about the cBioPortal clinical file format here.
-o | --target-file: This is the path to the target clinical file that will be generated. It will contain mapped OncoTree codes from <source_oncotree_version>-to-<target_oncotree_version>.
-s | --source-version: This is the source OncoTree version. The OncoTree codes in the source file must correspond to this version.
-t | --target-version: This is the target OncoTree version that the script will attempt to map the source file OncoTree codes to.
The list of OncoTree versions available are viewable here or on the dropdown menu of the OncoTree home page.
Note: the source file should not contain embedded line breaks within any single cell in the table, such as those created by using the keyboard combinations Alt-Enter or Command-Option-Enter while editing a cell in Microsoft Excel.
For a detailed walkthrough of running the tool, see the "Tutorial" section below.
The OncoTree Mapper Tool will automatically replace the value in the ONCOTREE_CODE column with the mapped code if available. The tool will also add a new column called ONCOTREE_CODE_OPTIONS containing suggestions for OncoTree codes if one or more nodes could not be directly mapped. The ONCOTREE_CODE_OPTIONS column formats its suggestions differently depending on the mapping results. Possible suggestion formats and corresponding examples are shown below.
Unambiguous direct mappings occur when an OncoTree code maps directly to a single code in the target version. In this case, the ONCOTREE_CODE_OPTIONS column will be left blank, and the mapped code will be automatically placed in the ONCOTREE_CODE column. Unambiguous direct mappings are checked for addition of more granular nodes; to see how this may affect the ONCOTREE_CODE_OPTIONS column formatting, please refer to the subsection below "4. More Granular Nodes Introduced".
Ambiguous direct mappings occur when an OncoTree code maps to multiple codes in the target version. The ONCOTREE_CODE_OPTIONS column formats the output as follows:
'Source Code' -> {'Code 1', 'Code 2', 'Code 3', } e.g. ALL -> {TLL, BLL}
Example: Schema describing the revocation of OncoTree node ALL is mapped to multiple nodes.
In oncotree_2018_05_01, ALL had two children: TALL and BALL. On release oncotree_2018_06_01, the ALL node was discontinued and the TALL node was renamed TLL and the BALL node was renamed BLL.
The ONCOTREE_CODE_OPTIONS column would be shown as follows:
ALL -> {TLL, BLL}
Ambiguous direct mappings are also checked for addition of more granular nodes; to see how this may affect the ONCOTREE_CODE_OPTIONS column formatting, please refer to the subsection below "4. More Granular Nodes Introduced".
No direct mappings occur when the source OncoTree code is unrelated to any OncoTree code in the target version. One such possibility is mapping a newly introduced OncoTree code backwards in time. In this case, the tool finds the closest set of neighbors (e.g parents and children) which are mappable in the target version. The ONCOTREE_CODE_OPTIONS column returns the set with the keyword Neighbors as follows:
Example: Schema describing a case where new OncoTree node UPA cannot be directly mapped backwards to a node.
In oncotree_2019_03_01, UPA was added to the OncoTree as a child node of BLADDER. Because UPA did not exist in previous version oncotree_2018_05_01 and did not replace any existing node, the tool uses the surrounding nodes when mapping backwards. In this case, the parent node BLADDER is returned as the closest match.
The ONCOTREE_CODE_OPTIONS column would be shown as follows:
In certain cases, the target version can also introduce nodes with more specific descriptions. When this occurs, the tool will add the string more granular choices introduced to the existing text in the ONCOTREE_CODE_OPTIONS column as follows:
'Source Code' -> {'Code 1', }, more granular choices introduced e.g. TALL -> {TLL}, more granular choices introduced
Example: Schema describing a case where OncoTree node TALL is mapped to a node with more granular children
In oncotree_2019_03_01, TALL was a leaf node with no children. In release oncotree_2019_06_01, TLL was introduced as a replacement for TALL with additional children ETPLL and NKCLL.
The ONCOTREE_CODE_OPTIONS column would be shown as follows:
An invalid source OncoTree Code means the provided code cannot be found in the source version. In such a case, mapping cannot be attempted and the ONCOTREE_CODE_OPTIONS column displays the following:
'Source Code' -> ???, OncoTree code not in source OncoTree version
The following tutorial will guide the user through using the oncotree_to_oncotree.py tool. The tutorial will go through the expected output to highlight specific mapping cases. Additionally, the tutorial will cross-reference the output with the generated mapping summary to demonstrate how it can be used to aid in manual selection of unresolved nodes.
The tool will output two files: data_clinical_sample_remapped.txt and data_clinical_sample_remapped_summary.html. For your reference, you can see the expected output files - here and here
Using values in the ONCOTREE_CODE_OPTIONS as a guide, manually select and place an OncoTree Code in the ONCOTREE_CODE column. For additional information, refer to the summary file data_clinical_sample_remapped_summary.html. Repeat for all rows in the output file. Several examples are shown below.
ALL -> {BLL,TLL}, more granular choices introduced
Source OncoTree code ALL maps directly to codes BLL and TLL. Users should place either BLL or TLL in the ONCOTREE_CODE column. The ONCOTREE_CODE_OPTIONS column also notes that more granular choices were introduced; as such, users can use the summary file for additional guidance.
Searching by source code, the following information can be found in the summary file:
The summary file provides a link to the closest shared parent node LNM; users can choose more granular nodes by referencing the provided tree:
Source OncoTree code BALL maps directly to BLL. Users should place BLL in the ONCOTREE_CODE column. However, similar to sample 1, the ONCOTREE_CODE_OPTIONS indicates there are more granular choices available. Users can follow the same steps as above and use the summary file to select a more granular node.
No additional resolution is needed; the previous OncoTree code was already automatically mapped to PTCL and placed in the ONCOTREE_CODE column. ONCOTREE_CODE_OPTIONS is empty because no manual selections were necessary.
HGNEE -> ???, OncoTree code not in source OncoTree version
Source OncoTree code HGNEE was not found in the source OncoTree version and therefore could not be mapped. Users can either reassign a new source OncoTree code (and rerun the script) or remove the sample.
After filling in the ONCOTREE_CODE column with an OncoTree code for each sample, use an editor (e.g. Microsoft Excel, vim, etc.) to trim off the ONCOTREE_CODE_OPTIONS column. The resulting file will be a new data_clinical_sample.txt file with all codes mapped to the target version. The first four columns of the final result is shown below:
The Ontology Mapping tool was developed to facilitate the mapping between different cancer classification systems. We currently support mapping between OncoTree, ICD-O, NCIt, UMLS and HemeOnc systems. The tool and the mapping file (the mapping file does not need to be downloaded to run the tool) can be found here
i | --source-file: This is the source file path. The source file must contain one of the ONCOTREE_CODE, NCIT_CODE, UMLS_CODE, ICDO_TOPOGRAPHY_CODE, ICDO_MORPHOLOGY_CODE or HEMEONC_CODE in the file header and it must contain codes corresponding to the Ontology System.
o | --target-file: This is the path to the target file that will be generated. It will contain ontologies mapped from source code in <source-file> to <target-code>.
s | --source-code: This is the source ontology code in <source-file>. It must be one of the ONCOTREE_CODE, NCIT_CODE, UMLS_CODE, ICDO_TOPOGRAPHY_CODE, ICDO_MORPHOLOGY_CODE or HEMEONC_CODE.
t | --target-code: This is the target ontology code that the script will attempt to map the source file ontology code to. It must be one of the ONCOTREE_CODE, NCIT_CODE, UMLS_CODE, ICDO_TOPOGRAPHY_CODE, ICDO_MORPHOLOGY_CODE or HEMEONC_CODE.
Note
The source file should be tab delimited and should contain one of the ontology: ONCOTREE_CODE, NCIT_CODE, UMLS_CODE, ICDO_TOPOGRAPHY_CODE, ICDO_MORPHOLOGY_CODE or HEMEONC_CODE in the file header.
We currently are allowing only one ontology to another ontology mapping. In the future, we plan to extend the tool to support mapping to multiple ontology systems.
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New Stable Release OncoTree version oncotree_2021_11_02 is now the latest stable release. The previous stable version is still accessible as version oncotree_2020_10_01.
New nodes added:
Desmoplastic/Nodular Medulloblastoma, NOS (DMBLNOS)
Medulloblastoma with Extensive Nodularity, NOS (MBENNOS)
Medulloblastoma with Extensive Nodularity, SHH Subtype (MBENSHH)
Pancreatic Neuroendocrine Carcinoma (PANEC) in the original version of this news release this node was accidentally omitted
Nodes reclassified
The following list of oncotree codes had the mainType shortened to drop the suffix "NOS": ADRENAL_GLAND, AMPULLA_OF_VATER, BILIARY_TRACT, BLADDER, BONE, BOWEL, BRAIN, BREAST, CERVIX, EYE, HEAD_NECK, KIDNEY, LIVER, LUNG, LYMPH, MYELOID, OTHER, OVARY, PANCREAS, PENIS, PERITONEUM, PLEURA, PNS, PROSTATE, SKIN, SOFT_TISSUE, STOMACH, TESTIS, THYMUS, THYROID, UTERUS, VULVA
Cholangiocarcinoma (CHOL) now has direct parent Intraductal Papillary Neoplasm of the Bile Duct (IPN) [previously: Biliary Tract (BILIARY_TRACT)]
Gallbladder Cancer (GBC) now has direct parent Intracholecystic Papillary Neoplasm (ICPN) [previously: Biliary Tract (BILIARY_TRACT)]
oncotree candidate release version additions:
Three new nodes intended only for version oncotree_candidate_release were added (NVRINT, MPNWP, MDSWP). These nodes will not be incorperated into oncotree latest stable.
resources added
rdf formatted OWL ontology and taxomomy files for recent oncotree versions have been added to our github repository. They can be explored here .
The Ontology Mapping tool was developed to facilitate the mapping between different cancer classification systems. We currently support mapping between OncoTree, ICD-O, NCIt, UMLS and HemeOnc systems.
A mapping file containing mappings between the different ontologies and OncoTree codes as well as a python script to run the mapping is available on the OncoTree GitHub page . Details are also available on the Mapping Tools page .
The mapping file is expected to grow as we curate more ontology mappings for OncoTree codes.
New Stable Release OncoTree version oncotree_2020_10_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2020_04_01.
New nodes added:
Basal Cell Carcinoma of Prostate (BCCP)
Node deleted:
Porphyria Cutania Tarda (PCT)
Node with updated name:
Goblet Cell Adenocarcinoma of the Appendix (GCCAP) [previously: Goblet Cell Carcinoid of the Appendix (GCCAP)].
New Stable Release OncoTree version oncotree_2020_04_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2020_02_06.
New nodes added:
AML with Variant RARA translocation (AMLRARA)
Nodes reclassified:
Mixed Cancer Types (MIXED is now a child of Other (OTHER) [previously under: Cancer of Unknown Primary (CUP)].
When providing web links to oncotree, you may include a search term as an optional argument and the oncotree you reference will be displayed with the search term located and highlighted. Use of this mechanism can be seen in the example output for the OncoTree-to-OncoTree code mapping tool.
As an example, you can provide a direct link to the TumorType node PANET in oncotree version oncotree_2019_12_01 with this link: http://oncotree.mskcc.org/#/home?version=oncotree_2019_12_01&search_term=(PANET)
New Stable Release OncoTree version oncotree_2020_02_06 is now the latest stable release. The previous stable version is still accessible as version oncotree_2020_02_01.
Nodes reclassified:
Gallbladder Cancer (GBC) is now a child of Biliary Tract (BILIARY_TRACT) [previously under: Intracholecystic Papillary Neoplasm (ICPN)].
Cholangiocarcinoma (CHOL) is now a child of Biliary Tract (BILIARY_TRACT) [previously under: Intraductal Papillary Neoplasm of the Bile Duct (IPN)].
New Stable Release OncoTree version oncotree_2020_02_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2019_12_01.
New nodes added:
Intraductal Oncocytic Papillary Neoplasm (IOPN)
Intraductal Tubulopapillary Neoplasm (ITPN)
Intracholecystic Papillary Neoplasm (ICPN)
Intraductal Papillary Neoplasm of the Bile Duct (IPN)
Nodes reclassified:
Gallbladder Cancer (GBC) is now a child of Intracholecystic Papillary Neoplasm (ICPN) [previously under: Biliary Tract (BILIARY_TRACT)].
Cholangiocarcinoma (CHOL) is now a child of Intraductal Papillary Neoplasm of the Bile Duct (IPN) [previously under: Biliary Tract (BILIARY_TRACT)].
New Stable Release OncoTree version oncotree_2019_12_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2019_08_01.
New Stable Release OncoTree version oncotree_2019_08_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2019_05_01.
New nodes added:
Lacrimal Gland Tumor (LGT)
Adenoid Cystic Carcinoma of the Lacrimal Gland (ACLG)
Squamous Cell Carcinoma of the Lacrimal Gland (SCLG)
New Stable Release OncoTree version oncotree_2019_05_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2019_03_01.
Nodes reclassified
Intestinal Ampullary Carcinoma (IAMPCA) MainType is now Ampullary Cancer [previously: Ampullary Carcinoma]
Mixed Ampullary Carcinoma (MAMPCA) MainType is now Ampullary Cancer [previously: Ampullary Carcinoma]
Pancreatobiliary Ampullary Carcinoma (PAMPCA) MainType is now Ampullary Cancer [previously: Ampullary Carcinoma]
Ependymoma (EPM) MainType is now Glioma [previously: CNS Cancer]
Rosai-Dorfman Disease (RDD) MainType is now Histiocytosis [previously: Histiocytic Disorder]
The OncoTree-to-OncoTree mapping tool (now version 1.1) has been slightly improved, mainly by adding a separate section in the output summary for reporting OncoTree codes which were replaced automatically. Also, additional documentation and description of the tool has been added under the "Mapping Tools" tab.
A python program is now available for download under the webpage tab labeled "Mapping Tools". This tool will rewrite OncoTree codes in a tabular clinical data file, mapping from one version of OncoTree to another. When additional guidance is necessary, the program will insert a column containing options and comments next to the ONCOTREE_CODE column. After selecting an appropriate OncoTree code for cases which require action, this extra column can be deleted to produce a fully re-mapped clinical data file. More details about this tool and how to use it are available under the "Mapping Tools" tab.
The OncoTree-to-OncoTree mapping tool relies on an expanded model of OncoTree node history. This is reflected in the Web API schema for Tumor Types, which now has added properties called "precursors" and "revocations". Using these properties, and the existing "history" property, the tool is able to make proper mappings across OncoTree versions, and give suggestions when no clear mapping is available. It is also reflected in the main tree visualization of OncoTree, where a combination of these properties (when set) will be displayed in the pop-up information box with label "Previous Codes".
New Stable Release OncoTree version oncotree_2019_03_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2019_02_01.
Development of a tool to map OncoTree codes between different versions of OncoTree is nearing completion.
Related to this, users of the OncoTree Web API should be aware that we will soon be adding two additional properties to the output schema returned by the api/tumorTypes endpoints. The properties "precursors" and "revocations" will be added alongside the "history" property (having the same type: an array of strings). These will help distinguish the kinds of possible relationships to OncoTree nodes in prior versions of OncoTree. We expect this new schema to be backwards compatible, but if your language or tools requires an exactly matching JSON schema you will need to make adjustments.
New Stable Release OncoTree version oncotree_2019_02_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2018_11_01.
New Stable Release OncoTree version oncotree_2018_11_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2018_09_01.
New nodes added:
Gastrointestinal Neuroendocrine Tumors of the Esophagus/Stomach (GINETES)
High-Grade Neuroendocrine Carcinoma of the Esophagus (HGNEE)
High-Grade Neuroendocrine Carcinoma of the Stomach (HGNES)
Nodes reclassified:
Well-Differentiated Neuroendocrine Tumors of the Stomach (SWDNET) is now a child of Gastrointestinal Neuroendocrine Tumors of the Esophagus/Stomach (GINETES) [previously under: Bowel (BOWEL)].
New Stable Release OncoTree version oncotree_2018_09_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2018_08_01.
New Stable Release OncoTree version oncotree_2018_08_01 is now the latest stable release. The previous stable version is still accessible as version oncotree_2018_07_01.
New nodes added:
Angiomatoid Fibrous Histiocytoma (AFH)
Clear Cell Sarcoma of Kidney (CCSK)
Ewing Sarcoma of Soft Tissue (ESST)
Extra Gonadal Germ Cell Tumor (EGCT)
Infantile Fibrosarcoma (IFS)
Malignant Glomus Tumor (MGST)
Malignant Rhabdoid Tumor of the Liver (MRTL)
Myofibromatosis (IMS)
Sialoblastoma (SBL)
Undifferentiated Embryonal Sarcoma of the Liver (UESL)
New Stable Release OncoTree version oncotree_2018_07_01 is now the latest stable release. The previous stable version is still accessible through the OncoTree web API by requesting version oncotree_2018_06_15.
New Stable Release OncoTree version oncotree_2018_06_15 is now the latest stable release. The previous stable version is still accessible through the OncoTree web API by requesting version oncotree_2018_06_01.
Nodes reclassified
Mature B-Cell Neoplasms (MBN) and Mature T and NK Neoplasms (MTNN) and their subnodes were relocated to be under Non-Hodgkin Lymphoma (NHL).
Rosai-Dorfman Disease (RDD) was relocated to be under Histiocytic and Dendritic Cell Neoplasms (HDCN). Previously RDD was under Lymphoid Neoplasm (LNM) in the Lymphoid category.
New Stable Release OncoTree version oncotree_2018_06_01 is now the latest stable release. The previous stable version is still accessible through the OncoTree web API by requesting version oncotree_2018_05_01.
Blood and Lymph subtrees replaced with new Myeloid and Lymphoid subtrees:
23 nodes in the previous Blood subtree have been deleted or relocated/renamed. Affected OncoTree codes from this tree: BLOOD, BPDCN, HIST, LCH, ECD, LEUK, ALL, BALL, TALL, AMOL, AML, CLL, CML, CMML, HCL, LGLL, MM, MDS, MPN, ETC, MYF, PCV, SM
28 nodes in the previous Lymph subtree have been deleted or relocated/renamed. Affected OncoTree codes from this tree: LYMPH, HL, CHL, NLPHL, NHL, BCL, BL, DLBCL, MALTL, FL, MCL, MZL, MBCL, NMZL, PCNSL, PEL, SLL, SMZL, WM, TNKL, CTCL, MYCF, SEZS, PTCL, ALCL, AITL, PTCLNOS, RD
101 nodes in the current Myeloid subtree have been added or relocated/renamed from previous subtrees. OncoTree codes in this new subtree are: MYELOID, MATPL, MBGN, MNM, ALAL, AUL, MPALBCRABL1, MPALKMT2A, MPALBNOS, MPALTNOS, AML, AMLMRC, AMLRGA, AMLRBM15MKL1, AMLBCRABL1, AMLCEBPA, AMLNPM1, AMLRUNX1, AMLCBFBMYH11, AMLGATA2MECOM, AMLDEKNUP214, AMLRUNX1RUNX1T1, AMLMLLT3KMT2A, APLPMLRARA, AMLNOS, AM, AMLMD, AWM, ABL, AMKL, AMOL, AMML, APMF, PERL, MPRDS, MLADS, TAM, MS, TMN, TAML, TMDS, BPDCN, HDCN, JXG, ECD, FRCT, FDCS, HS, IDCT, IDCS, LCH, LCS, MCD, CMCD, MCSL, SM, ASM, ISM, SMMCL, SSM, SMAHN, MDS, MDSEB, MDSEB1, MDSEB2, MDSID5Q, MDSMD, MDSRS, MDSRSMD, MDSRSSLD, MDSSLD, MDSU, RCYC, MDS/MPN, aCML, CMML, CMML0, CMML1, CMML2, JMML, MDSMPNRST, MDSMPNU, MNGLP, MLNER, MLNFGFR1, MLNPCM1JAK2, MLNPDGFRA, MLNPDGFRB, MPN, CELNOS, CML, CMLBCRABL1, CNL, ET, ETMF, MPNU, PV, PVMF, PMF, PMFPES, PMFOFS
Nodes reclassified
Adrenocortical Adenoma (ACA) MainType is now Adrenocortical Adenoma [previously: Adrenocortical Carcinoma]
Ampulla of Vater (AMPULLA_OF_VATER) MainType is now Ampullary Cancer [previously: Ampullary Carcinoma]
Parathyroid Cancer (PTH) MainType is now Parathyroid Cancer [previously: Head and Neck Cancer]
Parathyroid Carcinoma (PTHC) MainType is now Parathyroid Cancer [previously: Head and Neck Cancer]
Follicular Dendritic Cell Sarcoma (FDCS) was moved from the Soft Tissue subtree into the Myeloid subtree with direct parent Histiocytic and Dendritic Cell Neoplasms (HDCN)
Interdigitating Dendritic Cell Sarcoma (IDCS) was moved from the Soft Tissue subtree into the Myeloid subtree with direct parent Histiocytic and Dendritic Cell Neoplasms (HDCN)
New nodes added:
Inverted Urothelial Papilloma (IUP)
Urothelial Papilloma (UPA)
Oncocytic Adenoma of the Thyroid (OAT)
Character set simplification
Salivary Gland-Type Tumor of the Lung (SGTTL) used to contain a unicode character for a horizontal dash. This punctuation mark is now a hyphen.
New Stable Release OncoTree version oncotree_2018_05_01 is now the latest stable release. The previous stable version is still accessible through the OncoTree web API by requesting version oncotree_2018_04_01.
New nodes added:
Primary CNS Melanocytic Tumors (PCNSMT)
Melanocytoma (MELC)
Node reclassified
Primary CNS Melanoma (PCNSM) now is a child of Primary CNS Melanocytic Tumors (PCNSMT) [previously under: CNS/Brain].
The /api/tumor_types.txt endpoint is now deprecated. It is scheduled for deletion as part of the next API version release.
Most endpoint paths in the API remain the same and provide the same services. Exceptions are:
/api/tumorTypes used to accept a query parameter ("flat") which controlled the output format for receiving a tree representation or a flat representation of the full set of TumorTypes. Now this endpoint always returns a flat list of all TumorTypes and a new endpoint path (/api/tumorTypes/tree) is used to retrieve a tree representation of the OncoTree. Previous requests which included "flat=false" should be adjusted to use the /api/tumorTypes/tree endpoint. Otherwise "flat=true" should be dropped from the request.
/api/tumorTypes used to accept a query parameter ("deprecated") which is no longer recognized. This parameter should be dropped from requests. Deprecated OncoTree codes can instead be found in the history attribute of the response.
the POST request endpoint (/api/tumorTypes/search) which accepted a list of TumorType queries has been deprecated and is no longer available through the swagger-ui interface. The GET request endpoint /api/tumorTypes/search/{type}/{query} remains available as before. If you previously submitted an array of query requests, you should iterate through the array and call the GET request endpoint to make one query per request.
The output format (schema) of many endpoints has been simplified. You will need to adjust your result handling accordingly. Changes include:
responses no longer include a "meta" element with associated code and error messages. Instead HTTP status codes are set appropriately and error messages are supplied in message bodies. Responses also no longer contain a "data" element. Objects representing the API output are directly returned instead.
MainType values are no longer modeled as objects. Each MainType value is now represented as a simple string. The /api/mainTypes endpoint now returns an array of strings rather than an object mapping MainType names to MainType objects.
TumorType values no longer contain elements "id", "deprecated", "links", "NCI", "UMLS". A new element ("externalReferences") has been added which contains a JSON object mapping external authority names to arrays of associated identifiers. Such as "externalReferences":
Argument validation has been strengthened for several parameters, such as "type" and "levels" in the /api/tumorTypes/search/{type}/{query} endpoint. Now improper arguments cause an a HTTP status response indicating error, with a description of the problem in the body.
New Stable Release OncoTree version oncotree_2018_04_01 is now the latest stable release. The previous stable version is still accessible through the OncoTree web API by requesting version oncotree_2018_03_01.
New Stable Release OncoTree version oncotree_2018_03_01 is now the latest stable release. The previous stable version is still accessible through the OncoTree web API by requesting version oncotree_2018_02_01.
New node added:
Ganglioneuroma (GN)
Node reclassified
Rhabdoid Cancer (MRT) now has direct parent Kidney (KIDNEY) [previously: Wilms' Tumor (WT)] Main type is now "Rhabdoid Cancer" [previously: Wilms Tumor]
OncoTree format expanded to support deeper tree nodes
To support upcoming expansion of the OncoTree, the 5 named levels of the OncoTree {Primary, Secondary, Tertiary, Quaternary, Quinternary} have been dropped in favor of level numbers {1, 2, 3, 4, 5, ...}. Web API functions have been adjusted accordingly, and an API function which outputs a table format of the OncoTree has been adjusted to output 7 levels of depth.
New Stable Release OncoTree version oncotree_2018_02_01 is now the latest stable release. The previous stable version is still accessible for use through version name oncotree_2018_01_01.
New nodes added:
Adenosquamous Carcinoma of the Gallbladder (GBASC)
Gallbladder Adenocarcinoma, NOS (GBAD)
Small Cell Gallbladder Carcinoma (SCGBC)
Juvenile Secretory Carcinoma of the Breast (JSCB)
Osteoclastic Giant Cell Tumor (OSGCT)
Peritoneal Serous Carcinoma (PSEC)
Nodes reclassified [from: Embryonal Tumor, to: Peripheral Nervous System]:
Ganglioneuroblastoma (GNBL)
Neuroblastoma (NBL)
Node with renamed OncoTree code:
Spindle Cell Carcinoma of the Lung (SPCC) [previously: SpCC]
OncoTree is a comprehensive, community-led cancer classification system that adapts to the evolving demands of precision oncology. Designed to classify cancers by both histological and molecular traits, it provides a structured framework to complement the clinical decision-making processes. The platform, which is open-source and publicly accessible, is governed by a diverse committee of oncologists, pathologists, and scientists. This multidisciplinary oversight ensures OncoTree remains relevant, incorporating new cancer types and research advancements in real time to support clinical decision-making and research applications.
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+import{_ as e,c as a,o,a3 as t}from"./chunks/framework.CyEiTwkJ.js";const r="/assets/curation_process.CwbRUQ02.png",b=JSON.parse('{"title":"About","description":"","frontmatter":{},"headers":[],"relativePath":"about.md","filePath":"about.md"}'),s={name:"about.md"},i=t('
OncoTree is a comprehensive, community-led cancer classification system that adapts to the evolving demands of precision oncology. Designed to classify cancers by both histological and molecular traits, it provides a structured framework to complement the clinical decision-making processes. The platform, which is open-source and publicly accessible, is governed by a diverse committee of oncologists, pathologists, and scientists. This multidisciplinary oversight ensures OncoTree remains relevant, incorporating new cancer types and research advancements in real time to support clinical decision-making and research applications.
