1.1

1.1.1

Version 1.1.1 is a patch release that modernizes the Cat-VRS build pipeline and advances its imported dependencies (VRS 2.1.1 and GKM Core 1.3.0). It also renames the Cat-VRS controlled vocabulary for relation and match-characteristic terms from ga4gh-gks-term to ga4gh-gkm-term. No change alters which instances validate against a trial use maturity class, and there are no additions or removals to the set of Cat-VRS product features.

Patch changes

The following product features at trial use maturity were modified without changing which instances validate:

  • Constraint: the abstract base is now declared sealed. The metaschema processor renders it as a closed union of its concrete subtypes with a type discriminator (matching the VRS abstract-class convention). The derived union is the same seven concrete subtypes that 1.1.0 listed by hand, and every subtype already required type. Categorical Variant constraints now references Constraint directly, which resolves to the same set.

  • The Canonical Allele and Protein Sequence Consequence recipes (and the draft Categorical CNV, Gene Fusion, and Function Variant recipes) now declare unevaluatedProperties: false. Every recipe already inherited closure from Categorical Variant, so the set of valid instances is unchanged.

  • The Cat-VRS controlled vocabulary is renamed from ga4gh-gks-term to ga4gh-gkm-term, following the GKS to GKM rename (#263). This changes the system recommended for relations and matchCharacteristic terms (for example ga4gh-gkm-term:allele-relation and ga4gh-gkm-term:location-match) in the Defining Allele Constraint and Defining Location Constraint guidance, in the Canonical Allele recipe (and the draft Categorical CNV recipe), and in the examples. The schemas do not enforce the system of these terms, so the set of valid instances is unchanged, but data written to the 1.1.0 guidance carries the earlier ga4gh-gks-term value.

Dependencies

  • The Cat-VRS schema identifier ($id) is now https://w3id.org/ga4gh/schema/cat-vrs/1.1.1/....

  • Imported schemas were advanced to VRS 2.1.1 and GKM Core 1.3.0. The only data-model changes in GKM Core 1.3.0 — a new optional ConceptSet.conceptSetType field and iriReference as a new allowed ConceptSet.concepts member — do not reach Cat-VRS: Cat-VRS uses MappableConcept, which 1.3.0 leaves unchanged, but not ConceptSet.

Supporting changes

The following supporting changes were made to Cat-VRS that do not impact the Cat-VRS data model:

  • Adopted the modernized GKM metaschema processor (ga4gh.gkm.metaschema 0.4.8), with which the source YAMLs are compiled (source2classes / source2splitjs / y2t). Cross-schema references in the recipe definitions now use explicit $refCurie (e.g. cat-vrs:CategoricalVariant), as required by the stricter 0.4.x processor.

  • Cat-VRS now generates and owns the documentation definitions for its imported VRS and GKM Core classes locally, rather than depending on the submodule’s pre-generated definitions. Imported VRS class pages link to the full definition in the latest VRS specification.

  • Renamed the “Data Model” documentation section to “Model” (consistent with VRS) and consolidated the Constraint documentation onto a single index page.

  • The pre-commit CI job now checks out submodules, matching the local hook, so schema regeneration is verified in CI.

1.1.0

Version 1.1.0 is the second release of the Categorical Variant Representation Specification. Since 1.0.0, we have introduced two new data classes, enhanced our documentation and repository tooling, and published a preprint on the specification.

News

  • The Categorical Variant Representation Specification manuscript has been submitted. Please cite our preprint.

Minor changes

The following product features at trial use maturity were modified:

Patch changes

The following product features at draft maturity were introduced:

The following supporting changes were made to Cat-VRS that do not impact Cat-VRS schemas: