GA4GH Variant Annotation Specification
Introduction
Overview
Components
Use Cases and Implementations
Scope and Development
Quick Start
Modeling Foundations
Core Class Hierarchy
Data Structures
Statement Structure
Evidence Line Structure
Study Result Structure
Role of Propositions
Propositions in Statements
Propositions in Evidence Lines
Profiles
Profiling Tasks
Profiling Example
Model
Entity
Agent
Contribution
Data Item
Data Set
Document
Evidence Line
Genetic Context Variant Proposition
Information Entity
Mappable Concept
Method
Proposition
Statement
Data Structure
Implementation Guidance
1. Statement and Proposition Semantics
2. Attaching Evidence to a Statement
3. Use of the
Proposition.qualifier
Attribute:
Study Group
Study Result
Subject Variant Proposition
Element
Coding
Concept Mapping
Extension
Data Types
code
date
datetime
iriReference
Domain Entities
Condition
Condition Set
Gene
Therapy
Therapy Group
Variation
Profiles
Base Profiles
Proposition Profiles
Variant Pathogenicity Proposition
Variant Oncogenicity Proposition
Variant Clinical Significance Proposition
Variant Therapeutic Response Proposition
Variant Diagnostic Proposition
Variant Prognostic Proposition
Experimental Variant Functional Impact Proposition
Gene Disease Validity Proposition
Variant Molecular Consequence Proposition
Study Result Profiles
Cohort Allele Frequency Study Result
Experimental Variant Functional Impact Study Result
Tumor Variant Frequency Study Result
Computational Variant Functional Impact Analysis Result
Community Profiles
AMP/ASCO/CAP 2017 Aligned Profiles
Variant Clinical Significance Statement (AAC 2017)
Variant Amp/Asco/Cap Evidence Line (AAC 2017)
Variant Diagnostic Evidence Line (AAC 2017)
Variant Prognostic Evidence Line (AAC 2017)
Variant Therapeutic Evidence Line (AAC 2017)
ACMG 2015 Aligned Profiles
Variant Pathogenicity Statement (ACMG 2015)
Variant Pathogenicity Evidence Line (ACMG 2015)
CCV 2022 Aligned Profiles
Variant Oncogenicity Statement (CCV 2022)
Variant Oncogenicity Evidence Line (CCV 2022)
JSON Schema Catalog
Reference Implementation
Developer Guide
Profile Definition Mechanisms
Authoring Base vs Community Profiles
Custom Profile Development
Examples
ACMG Variant Pathogenicity Statement Example
ACMG Variant Pathogenicity Statement Example (with Evidence)
Custom Variant Pathogenicity Statement Example
Getting Involved
Releases
1.1
1.1.0
Minor Version Increment
Subject / object / focus model change
Statement enriched to carry evidence assessments
Patch Version Increment
Draft classes and community profiles
Pipeline modernization
Dependency / version refresh
1.0
1.0.1
Summary of Changes
1.0.0
Major Changes
Minor Changes
Appendices
SEPIO Modeling Framework
Design Decisions
Definition of ‘Variant Annotation’
Scope of Variant Knowledge Supported
Explicit Statement Semantics
Use of Propositions
Domain Entity Representation
Profile Authoring Mechanisms
The GKM Metaschema Processor
What It Does
Authoring Conventions the Processor Understands
Role in Testing
Role in Documentation
Version Pinning
See Also
Implementations
Variant Congruence
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
Major Version Increment
Minor Version Increment
Patch Version Increment
Releases
Pre-releases
Decision-maker roles
Feature Developers
Product Implementers
Product Owners
Work Stream Leads
Imported Data Types & Classes
VRS
Ga4ghIdentifiableObject
sequenceString
Residue
MolecularVariation
Allele
Relative Allele
Systemic Variation
Copy Number Count
Copy Number Change
Derivative Molecule
Cis Phased Block
Traversal Block
Terminus
Adjacency
Location
SequenceLocation
Sequence Offset Location
Relative Sequence Location
SequenceReference
Expression
SequenceExpression
Length Expression
Literal Sequence Expression
Reference Length Expression
Range
Cat-VRS
CategoricalVariant
Constraint
Defining Allele Constraint
Defining Location Constraint
Copy Count Constraint
Copy Change Constraint
Feature Context Constraint
Function Constraint
Adjacency Constraint
Functional Domain
Unspecified Element
GKM-Core
Concept Set
GA4GH Variant Annotation Specification
Index
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Index