Categorical CNV

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

A representation of the constraints for matching knowledge about CNVs.

Information Model

A CategoricalCNV is a Categorical Variant with exactly two constraints:

  1. A Defining Location Constraint with the .relations array containing only a liftover_to code.

  2. A Copy Change Constraint or Copy Count Constraint.

Examples

The following example Categorical Variants satisfy this Recipe:

Implementation Guidance

Constraints

Categorical Variants that are intended to represent Categorical Copy Number Variants must only contain two constraints. While the choice of using a Copy Change Constraint or Copy Count Constraint will depend on the type of Copy Number Variant intended to be expressed, the Defining Location Constraint is required to contain the following coding as a relations:

Warning

Some terms use the system ga4gh-gks-term. This is an internally controlled vocabulary used specifically within the Categorical Variant Representation Specification. We may add more terms in the future. If you would like to recommend a new term, please open a Discussion to suggest one!

Code

System

Rationale

liftover_to

ga4gh-gks-term:allele-relation:allele-relation

To specify that VRS objects that are listed as members may have a Sequence Location that is a liftover to another reference genome of the Defining Sequence Location.

The matchCharacteristic attribute is required within a Defining Location Constraint and is a MappableConcept, meaning that it should be represented using a term from an ontology. This attribute describes how a member’s Sequence Location must relate to the Defining Sequence Location in order to satisfy the constraint.

Note

matchCharacteristics are definitional and thus do alter the scope of the Categorical Variant’s definition. In other words, they do restrict which variants satisfy the Categorical Variant’s constraints.

Warning

Some terms use the system ga4gh-gks-term. This is an internally controlled vocabulary used specifically within the Categorical Variant Representation Specification. We may add more terms in the future. If you would like to recommend a new term, please open a Discussion to suggest one!

Coding

Rationale

ga4gh-gks-term:location-match:is_within

Used when the member’s Sequence Location is entirely within the Defining Sequence Location . A narrow match.

We recommend the following resources for constructing Sequence Location objects:

  • vrs-python is a Python package and reference implementation for VRS that can be used to generate VRS digests.

  • SeqRepo provides access to reference sequences and can be used to obtain Sequence Reference information, such as names and aliases, when constructing Sequence Reference objects directly.

Note

While neither the moleculeType nor residueAlphabet are required attributes for a Sequence Reference, we strongly recommend populating them within your implementation to clearly communicate to users what type of sequence your SequenceReference exists upon. Consider the following values, depending on the type of SequenceReference expressed:

Sequence reference type

moleculeType

residueAlphabet

Genomic

genomic

na

RNA

RNA

na

mRNA

mRNA

na

Protein

protein

aa

For additional Implementation Guidance, please visit VRS’ page for the Sequence Location concept.

Members

When modeling a Categorical Copy Number Variant, members may be populated with VRS Copy Number Change or Copy Number Count objects that satisfy: