Vocab. CIViC

CIViC vocabulary

Overview

CIViC is an open access, open source, community-driven web resource for Clinical Interpretation of Variants in Cancer, available online at civicdb.org.

Sources

The source data is provided by https://civicdb.org/releases/main in tsv format.

The V2 GraphQL CIViC API will be used to make the source retrieval and vocabulary maintenance efficient.

Transformation

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

Concept Names

All Concepts’ names are coming from the variant source table field.

Concept Code

All Concepts’ codes are coming from the variant_id source table field.

Standard Concepts

All the CIViC concepts are not standard.

Domains

All the codes from CIViC are Measurement domain concepts.

Concept Classes

The CIViC concepts have a Variant Concept Class.

Concept Relationships

Hierarchy

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

Instructions for ETL

All CIViC concepts are non-Standard. That means they have to be mapped to the corresponding Standard Concepts using the CONCEPT_RELATIONSHIP table ("Maps to" records). Most of them are mapped to single Concepts, generating one-to-one records in the CONCEPT_RELATIONSHIP table, but some of them create multiple records.