GA4GH Variation Representation Specification
HEAD
Introduction
Quick Start
Concepts
Molecular Variation
Allele
Definition and Information Model
Example
Implementation Guidance
Adjacency
Definition and Information Model
Example
Implementation Guidance
Cis-Phased Block
Definition and Information Model
Example
Terminus
Definition and Information Model
Example
Derivative Molecule
Definition and Information Model
Components
Example
Systemic Variation
Copy Number Count
Definition and Information Model
Example
Copy Number Change
Definition and Information Model
Example
Locations and References
Location
Sequence Location
Sequence Reference
Sequence Expression
Literal Sequence Expression
Definition and Information Model
Example
Reference Length Expression
Definition and Information Model
Example
Length Expression
Definition and Information Model
Example
Additional Data Types
Abstract Classes
GA4GH Identifiable Object
Variation
Entity
Element
General Purposes Types
Extension
Mappable Concept
Concept Mapping
Coding
Primitive Types
Range
residue
sequenceString
code
iriReference
Conventions
Required External Data
Contexts
Data Services
Suggested Implementation
Examples
Normalization
General Normalization Rules
Allele Normalization
LiteralSequenceExpression Alleles
Adjacency Normalization
Computed Identifiers
Requirements
Digest Serialization
Truncated Digest (sha512t24u)
Identifier Construction
References
Example
Translate HGVS to VRS
Generate a computed identifier
What’s Next?
Releases
2.0
2.0.0
Major Changes
2.0.1
Summary of Changes
1.3
1.3.0
News
Major Changes
Minor Changes
1.2
1.2.0
News
Important
Major Changes
Minor Changes
1.1
1.1.2
1.1.1
1.1.0
New classes
Other data model changes
Documentation changes
1.0
1.0.0
Appendices
Class Diagram
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
GA4GH Computed Identifier Alignment
Background
VRS Convention
GA4GH Inherent Properties
GA4GH Type Prefixes
Administration
Resource Identifiers
Truncated Digest Timing and Collision Analysis
Conclusions
Digest Timing
Collision Analysis
References
Background: The Birthday Problem
Approximation #1: Taylor approximation of terms of P’
Approximation #2: Taylor approximation of P’
Approximation #3: Square approximation
Summary of equations
Choosing a digest size
For completeness:
digest length (bytes) required for expected collision probability
\(P\)
over
\(m\)
messages
Design Decisions
GA4GH Inherent Properties over Value Objects
IRIs over CURIEs
IRI-References over IRIs
VRS identifier syntax and versioning
Use of value sets for VRS computed digests
Glossary
GA4GH Variation Representation Specification
Appendices
Edit on GitHub
Appendices
Class Diagram
GKS Maturity Model
Feature Maturity levels
Product Versioning and Releases
Decision-maker roles
GA4GH Computed Identifier Alignment
Background
VRS Convention
GA4GH Type Prefixes
Resource Identifiers
Truncated Digest Timing and Collision Analysis
Conclusions
Digest Timing
Collision Analysis
Choosing a digest size
Design Decisions
GA4GH Inherent Properties over Value Objects
IRIs over CURIEs
IRI-References over IRIs
VRS identifier syntax and versioning
Use of value sets for VRS computed digests
Glossary