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v0.7.0
- Add
bioevidence review(check,agreement,adjudication-sheet,score,freeze)
implementing the gold-standard protocol: strict annotation checks, Krippendorff's α with
bootstrap interval and Cohen's κ (both cross-checked against reference implementations),
adjudication of disagreements, scoring on the test split with hash-bound joins, and frozen
manifests. It never produces labels. - Add a blinded ClinVar expert-review kit (
evaluation/clinvar_review/): all 95 variants where
the validator and NCBI disagree plus 95 stratum-matched controls, an Excel workbook with
dropdowns, a reviewer rubric, a private key, and an importer into the protocol format. - CI runs ruff and mypy, and enforces a 95% test-coverage minimum (currently 98%).
- Add CONTRIBUTING, CODE_OF_CONDUCT (Contributor Covenant 2.1), SECURITY, issue forms and a
pull request template. - Add
community/profiles/: contributed domain profiles whose example cases are built,
validated and checked against expected outcomes in CI;_template/to copy. - Add a documentation site (MkDocs, strict link checking) published to GitHub Pages.
- The canine 0.3 implementation is also preserved at the
canine-0.3tag. - No change to validation decisions or report format; both benchmarks reproduce 0.6.0 exactly
apart fromvalidator_version.
Also in this release: 0.6.0 (not published separately)
0.6.0 was never released on its own, so upgrading from 0.5.0 also brings:
- A second real-data case, ClinVar germline classifications: 5,026 variants from the 2023-09 release validated with a ClinVar-style profile, compared with NCBI's own review status (98–99% agreement) and with 2026-09 outcomes. Where the validator is stricter, classifications were about 4–5× more likely to be reclassified or in conflict three years later (1★ and 2★).
docs/STANDARDS.mdmapping the record model to ECO, Biolink 4.4.4, GA4GH VA-Spec 1.0.1 and PROV-O; ECO meanings onExtractionMethodin the LinkML schema.
See the CHANGELOG for details.