OncoTree

Overview

This vocabulary 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.

Sources

The source data is provided by the OncoTree team and is retrieved using the OncoTree API and subsequently converted to source tables in the Vocabulary server.

Transformation

The procedures for transforming Concepts from the source format to the OMOP Standard Vocabularies can be found on the OHDSI GitHub.

Concept Names

All Concepts are assigned the Full Source Name.

Concept Code

Concept codes are taken from the "Code" field such as “ACA” for Adrenocortical Adenoma.

Standard Concepts

All Concepts in OncoTree are non-standard.

Domains

All concepts are in the Condition domain.

Concept Classes

The OncoTree concepts are all composed from the Condition Concept Class.

Concept Relationships

Internal Relationships

The OncoTree internal hierarchical relationships are preserved in the form of “Is a” and “subsumes” relationships.

External Relationships

The OncoTree concepts mostly have classic non-Standard to Standard mappings (Maps to). In addition, to indicate equivalence between the concepts, there are also “OncoTree to ICDO equivalent” when two concepts are equivalent and “OncoTree to ICDO broader”, when the ICDO concept is broader, i.e. describes a more generic term.

Hierarchy

Oncotree Concepts are non-Standard Concepts and therefore do not participate in the hierarchy of the CONCEPT_ANCESTOR table.

Instructions for ETL

All OncoTree concepts are non-Standard. That means they should all ideally be mapped to the corresponding Standard Concepts using the CONCEPT_RELATIONSHIP table ("Maps to" and occasionally "Maps to value" records). Most of them are mapped to single ICD-O or SNOMED concepts, generating one-to-one records in the Condition table, but some of them are mapped to several concepts creating multiple records.