GA4GH Categorical Variation Representation Specification
Introduction
Background and Problem Statement
Challenges to Unifying the Representation of Categorical Variants
Discussion
How Cat-VRS Works
Variant Matching and Knowledge Integration
Discussion
Getting Involved
Data Model
Categorical Variant
Constraint
Constraints
Adjacency Constraint
Definition and Information Model
Examples
Implementation Guidance
Copy Change Constraint
Definition and Information Model
Examples
Implementation Guidance
Copy Count Constraint
Definition and Information Model
Examples
Implementation Guidance
Defining Allele Constraint
Definition and Information Model
Examples
Implementation Guidance
Defining Location Constraint
Definition and Information Model
Examples
Implementation Guidance
Feature Context Constraint
Definition and Information Model
Examples
Implementation Guidance
Function Constraint
Definition and Information Model
Examples
Implementation Guidance
Recipes
Canonical Allele
Definition and Information Model
Examples
Implementation Guidance
Categorical CNV
Definition and Information Model
Examples
Implementation Guidance
Function Variant
Definition and Information Model
Examples
Implementation Guidance
Gene Fusion
Definition and Information Model
Examples
Implementation Guidance
Protein Sequence Consequence
Definition and Information Model
Examples
Implementation Guidance
Imported Data Types & Classes
VRS
Allele
Copy Number Count
Copy Number Change
Expression
Locations and References
Range
Sequence Expression
Terminus
Variation
GKS Core
Coding
ConceptMapping
ConceptSet
Element
Entity
Extension
MappableConcept
code
iriReference
Implementation Guide
Releases
1.0
1.0.0
Appendices
GKS Maturity Model
Feature Maturity levels
Developing a Draft Product Feature
Advancing from Draft to Trial Use
Advancing from Trial Use to Normative
Product Versioning and Releases
Versioning examples
Releases
Decision-maker roles
Feature Developers
Product Implementers
Product Leads
Work Stream Leads
Design Decisions
Major Impact
Treatment of CatVars as ((Hyper)intensional) Set-Theoretic Objects
Adoption of a Constraint-Based Model Instead of a Fixed Top-Down Typology of Data Classes
Medium Impact
Constraints as an Array of implicitly ANDed elements
Including Recipes in the Cat-VRS Specification
Machine Readable Specifications
Separating CopyNumberConstraint into CopyCountConstraint and CopyChangeConstraint
Separating DefiningContextConstraint into DefiningAlelleConstraint and DefiningLocationConstraint
Utilization of semantic versioning and the GKS maturity model
Generalization of GeneContextConstriant into FeatureContextConstraint
Minor Impact
Distinction between Relations and Mappings
Inclusion of Members as non-exhaustive array of contextual variants
Name as a non-required field
Renaming “Profiles” to “Recipes” to represent standard categorical variants templates
Handling of Function Variants using Müller’s Morphs
Integration of Mappable Concepts for Variant Relations
Error handling is intentionally unspecified and delegated to implementation.
Text casing
Product Roadmap
Active
Planned
Complete
Treatment of CatVars as ((Hyper)intensional) Set-Theoretic Objects
Catvars as Sets
Catvars as Intensional Sets
Catvars as Hyperintensional Set Objects
GA4GH Categorical Variation Representation Specification
Appendices
Edit on GitHub
Appendices
GKS Maturity Model
Feature Maturity levels
Product Versioning and Releases
Decision-maker roles
Design Decisions
Major Impact
Medium Impact
Minor Impact
Product Roadmap
Active
Planned
Complete
Treatment of CatVars as ((Hyper)intensional) Set-Theoretic Objects
Catvars as Sets
Catvars as Intensional Sets
Catvars as Hyperintensional Set Objects