The OncoTree is an open-source ontology that was developed at Memorial Sloan Kettering Cancer Center (MSK) for standardizing cancer type diagnosis from a clinical perspective by assigning each diagnosis a unique OncoTree code.
OncoTree codes are linked to every study imported into the cBioPortal for Cancer Genomics, where each sample is annotated with its own OncoTree code corresponding to its respective cancer type.
These codes are also used by OncoKB, a precision oncology knowledge base developed at MSK containing information about the effects and treatment implications of specific cancer gene alterations.
Read about our latest developments on our News page.
Users may submit their OncoTree related questions to the OncoTree Users Google Group.
All of the frontend code can be found at /web/src/main/javascript. The only configuration needed is to set ONCOTREE_BASE_URL
in constants.ts. During development, it may be easiest to simply point to the public instance of
OncoTree.
Make sure you are using node version >=20.12.2.
To begin development run:
cd ./web/src/main/javascript
npm install && npm run dev
The frontend must be transpiled to static assets before bundling into a jar. To do this follow the following steps:
-
Ensure that the correct
ONCOTREE_BASE_URLis specified in constants.ts. -
Run the following:
cd ./web/src/main/javascript npm install && npm run build -
The frontend assets are now up to date, and you are ready to bundle the jar.
The OncoTree Mapping Tool was developed to facilitate the mapping of OncoTree codes between different OncoTree release versions. To learn more about the OncoTree Converter tool, please refer to the OncoTree Mapping documentation.
The OncoTree is an evolving ontology and as such has gone through several iterations since its conception to improve the standardization of cancer type diagnoses from a clinical perspective. As such, some nodes on the OncoTree possess a complex revision history whereas others have a much more simple revision history.
For APIs, please see the OncoTree Swagger page
This work is licensed under a Creative Commons Attribution 4.0 International License.
