Feature Context Constraint

Definition and Information Model

Warning

This data class is at a draft maturity level and may change significantly in future releases. Maturity levels are described in the GKS Maturity Model.

Computational Definition

The feature that members of this categorical variant are associated with.

Information Model

Some FeatureContextConstraint attributes are inherited from Constraint.

Field	Flags	Type	Limits	Description
type		string	1..1	MUST be “FeatureContextConstraint”
featureContext		MappableConcept	1..1	A feature identifier.

Examples

The following example Categorical Variants utilize this Constraint:

A representative example of this Constraint, from TP53 Loss:

      }
    },
    {
      "type": "FeatureContextConstraint",
      "featureContext": {
        "type": "MappableConcept",
        "id": "hgnc:11998",
        "name": "TP53",
        "conceptType": "Gene",
        "primaryCoding": {
          "id": "hgnc:11998",
          "name": "TP53",
          "system": "https://genenames.org",
          "code": "HGNC:11998",
          "iris": [
            "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/HGNC:11998"
          ]
        },
        "extensions": [
          {
            "name": "cytogenetic location",
            "value": "17p13.1"

Implementation Guidance

The featureContext attribute is required and is a MappableConcept, meaning that it should be represented using a term from an externally defined ontology. Specifically, we recommend using Codings based on the HUGO Gene Nomenclature Committee, as we have done within our Examples of this Constraint.

Note

Implementers use this constraint to represent genes, but it can also be used to represent protein markers, variant consequences, and other genomic features. If you are using this constraint for uses other than to represent genes, please let us know!

Genes

We recommend specifying conceptType as “Gene” and using a symbol from the HUGO Gene Nomenclature Committee (HGNC) as a primaryCoding.

The Gene Normalizer is a Python package and public REST instance that can be used to obtain Codings and Concept Mappings of gene concepts based on Ensembl, NCBI Gene, HGNC, and other data sources.