GA4GH GKS Standards¶
ClinVar-GKM represents ClinVar data using the GKM (Genomic Knowledge Model) schema set — VRS, Cat-VRS, and VA-Spec — curated by the GA4GH Genomic Knowledge Standards (GKS) workstream and built on shared GKM-Core classes. This page links each specification, its schema repository, and its official Python implementation, and notes how each is applied in this pipeline.
Specifications¶
| Standard | What it is | How ClinVar-GKM uses it | Specification | Schema repo | Python library |
|---|---|---|---|---|---|
| VRS — Variation Representation Specification | Extensible spec for representing and uniquely identifying biological sequence variation | Every variant receives a computable, digest-identified VRS identifier | vrs.ga4gh.org | ga4gh/vrs | ga4gh/vrs-python |
| Cat-VRS — Categorical Variation | A terminology and data model for describing categorical variation concepts | Variations are represented as Cat-VRS categorical variants with defining-allele constraints and expressions | cat-vrs.ga4gh.org | ga4gh/cat-vrs | ga4gh/cat-vrs-python |
| VA-Spec — Variant Annotation Specification | An information model for representing variant annotations (statements, propositions, evidence) | Every SCV, VCV, and RCV classification is a VA-Spec statement with explicit propositions, evidence, and provenance | va-spec.ga4gh.org | ga4gh/va-spec | ga4gh/va-spec-python |
| GKM-Core | Common classes and schemas shared by all GKS specifications (entities, MappableConcept, extensions, etc.) |
Underlies the shared building blocks used across VRS, Cat-VRS, and VA-Spec output | — | ga4gh/gkm-core | (bundled with the libraries above) |
Getting started with the standards¶
- GKM Starter Kit (site) — a single community-facing entry point that helps you understand and adopt the GKS/GKM standards in practice.
The three Python libraries above (vrs-python, cat-vrs-python, va-spec-python) let you parse ClinVar-GKM
bundle and Parquet records directly into the standards' validated models — see the planned
Starter-kit documentation page on the
Roadmap for worked examples.