GA4GH Categorical Variation Representation Specification Logo
  • 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
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