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
  • Quick Start
  • Getting Involved
  • Model
    • Categorical Variant
    • 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
        • Adjacency
        • Allele
        • CisPhasedBlock
        • Copy Number Change
        • Copy Number Count
        • DerivativeMolecule
        • Expression
        • Ga4ghIdentifiableObject
        • Locations and References
        • MolecularVariation
        • Range
        • RelativeAllele
        • RelativeSequenceLocation
        • residue
        • Sequence Expression
        • SequenceOffsetLocation
        • sequenceString
        • SystemicVariation
        • Terminus
        • TraversalBlock
        • Variation
      • GKM Core
        • Coding
        • ConceptMapping
        • ConceptSet
        • Element
        • Entity
        • Extension
        • MappableConcept
        • code
        • iriReference
    • Additional Data Types
      • FunctionalDomain
      • UnspecifiedElement
  • Implementation Guide
  • Examples
  • Releases
    • 1.1
      • 1.1.1
        • Patch changes
        • Dependencies
        • Supporting changes
      • 1.1.0
        • News
        • Minor changes
        • Patch changes
    • 1.0
      • 1.0.0
  • Appendices
    • GA4GH Maturity Model
      • Alignment with GA4GH Product Development Processes
      • Feature Maturity levels
        • Developing a Draft Product Feature
        • Advancing from Draft to Trial Use
        • Advancing from Trial Use to Normative
        • Data Class Inheritance and Property Maturity
        • Communicating Maturity Level
      • Product Versioning and Releases
        • Versioning examples
        • Releases
      • Decision-maker roles
        • Feature Developers
        • Product Implementers
        • Product Owners
        • 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

  • GA4GH Maturity Model
    • Alignment with GA4GH Product Development Processes
    • 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
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