Vocab. Cancer_Modifier

Cancer Modifier vocabulary

Overview

The vocabulary is designed to represent major cancer-related attributes such as staging and grading parameters, spread of disease characteristics (lymph nodes and metastasis), and additional histological and molecular characteristics of the tumor.

The attributes were derived from a variety of cancer-specific ontologies (NAACCR, NCIt etc).

Sources

The source data is provided by

1. NAACCR in XML format.
2. NCIt in FLAT format.
3. SNOMED.

Transformation

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

Concept Names

The majority of concept names inherits the name of the exact attribute from concept class combined with deduplicated, explicit atomic semantic units (coming from parsing of source concept names using different delimiters).

Concept Name	Attribute1	Attribute2	Attribute3	Attribute4	Attribute5
AJCC/UICC 6th clinical T2a Category	AJCC/UICC	6th	clinical	T2a	Category
Metastasis to acromion	Metastasis to	acromion

Concept Code

Being an de novo created OMOP Vocabulary the bigger part of concepts has OMOP-generated codes, while staging/grading concept codes are built in the same fashion as names.

Concept Code	Attribute1	Attribute2	Attribute3	Attribute4	Attribute5
c-6th_AJCC/UICC-T2a	AJCC/UICC	6th	clinical	T2a	Category

Distribution of valid Standard/Non-standard Concepts

Most of the concepts within the Cancer Modifier vocabulary are standard and valid entities.

concept_class_id	standard_concept	count
Dimension	S	18
Extension/Invasion	S	544
Histopattern	S	444
Margin	S	433
Metastasis	S	529
Morph Abnormality		15
Nodes	S	192
Qualifier Value		7
Staging/Grading	S	2629
Topography	S	518

Domains

The majority of Cancer Modifier concepts are in the “Measurement” domain.

Concept Classes

Status	Concept Class	Modeling parameters			Concept niche
		Hierarchical	Attributive	Precoordinated (self sufficient by default)	Episode triggering	Phenotyping of complex biological structures
proceeded	Dimension	✓	✓	X
	Metastasis	✓		✓	✓
	Staging/Grading	✓		✓	✓
Non-proceeded (sorted by priority decline)	Nodes	✓		✓	✓
	Histopattern					✓
	Margin
	Extension/Invasion
	Topography

Concept Relationships

Hierarchy

Cancer Modifier Concepts are Standard Concepts but do not participate in the hierarchy of the CONCEPT_ANCESTOR table because there are no links between them and other standard concepts.

Some concept classes have internal hierarchy to represent relationships between concepts, such as sites of metastatic spread, staging/grading parameters with different level of granularity .

Instructions for ETL

The Cancer Modifier are meant to be target concepts during most cancer-specific ETL conversions.

Additional documentation:

Cancer Modifier. Metastasis fact coverage

Cancer Modifier. Staging and Grading fact coverage