--- pretty_name: VariantHound Research Snapshot language: - en license: other size_categories: - 1M Research and educational use only. This snapshot is not a diagnostic dataset or medical device, and its rankings require expert review and experimental validation. ## Current contents The release contains: - three literature-grounded canine benchmark cases; - source and orthology provenance manifests; - a checksum-pinned Ensembl 116 dog-human-mouse orthology snapshot in releases built by the publication workflow; - a checksum pin for HPO 2026-09-01 and its matching human annotations, plus normalized JSONL in publication-workflow releases; - a dated Monarch 2026-09-02 evidence snapshot with a checksum-pinned HGNC stable-ID crosswalk; - a direct, retrieval-dated MGI genotype/phenotype snapshot with reconciled stable gene IDs; - a processed canine OMIA snapshot with phenes, stable-ID gene evidence, causal variants, breeds, and publications; - a compact PHENIO HP/MP/uPheno semantic-similarity closure with upstream ontology versions; - content-addressed browser shards for terms, phenotype closure, stable-ID gene profiles, and orthology; - machine-readable schemas for the published contracts; - evaluation, data, orthology, HPO, Monarch, MGI, OMIA, and PHENIO documentation; - a release manifest containing the source Git commit, byte sizes, and SHA-256 checksums. `data/benchmark_cases.jsonl` is the viewer-friendly benchmark split. HPO and OMIA are published as normalized JSONL under their source directories; raw upstream assets are not mirrored. The snapshot does not include raw OMIA, Monarch, MGI, Ensembl, or Dog10K database exports. ## Evaluation safety The benchmark metadata defines direct evidence and disease masks for discovery simulation. Temporal evaluation is allowed only when a historical source snapshot predating the case publication has been independently materialized. Known-evidence retrieval results must not be reported as discovery performance. ## Orthology status The publication workflow materializes 41,504 Ensembl 116 protein-tree orthology edges: 20,279 dog-human and 21,225 dog-mouse links. It unions the dog, human, and mouse genome-specific exports because Ensembl partitions pairwise rows arbitrarily between those files. Every artifact is checked against its pinned byte count, official MD5, and SHA-256 before transformation. One-to-many and many-to-many relationships are retained and explicitly marked ambiguous. ## HPO status The publication workflow verifies three immutable GitHub release assets before materializing 20,482 ontology terms, 333,983 human gene-phenotype annotations, and 286,651 disease-phenotype annotations. Negated disease annotations remain explicit. The snapshot is marked `current-snapshot-only` and cannot be used as a historical temporal-evaluation source. ## Monarch status The dated Monarch KG subsets materialize 6,965 deduplicated human gene-disease associations and 296,123 mouse gene-phenotype associations. Human HGNC IDs are resolved through a separately pinned HGNC export: 4,799 of 4,800 genes have Ensembl IDs and all 4,800 have a stable NCBI or Ensembl join ID. Primary and aggregator provenance are retained so MGI-derived rows cannot be double-counted when direct MGI data is added. ## Direct MGI status The direct MGI snapshot contains 15,317 MP terms and 283,119 genotype-phenotype rows. Identifier reconciliation makes 276,606 rows rank-eligible. It retains but excludes 26 rows affected by conflicting NCBI mappings and 6,487 rows whose markers lack stable join IDs. Direct MGI and Monarch's MGI-derived view must be deduplicated by provenance before scoring. ## OMIA status The retrieval-dated canine transform contains 1,019 phenes, 435 gene-phene edges, and 594 variants linked to single-locus traits. OMIA internal gene IDs are resolved only through the separately pinned official export: 430 gene-phene rows and 591 variant rows are rank-eligible, while unresolved mappings remain available for audit. Each evidence row includes deterministic discovery mask IDs. Because OMIA provides a moving dump rather than historical releases, this snapshot is restricted to current-snapshot evaluation. ## PHENIO status The pinned PHENIO `v2026-09-01` transform scans 82,128,289 materialized relations and retains 3,972,487 entailed reflexive subclass rows for 20,413 HPO, 15,317 MP, and 54,198 uPheno terms. This compact closure preserves the cross-species paths needed by deterministic semantic similarity while excluding unrelated integrated relations. The full upstream graph is not mirrored. ## Reproducibility Every uploaded release is built by `pipelines/build_hf_release.py`. Verify `release-manifest.json` before using the data. The manifest records every payload file and its SHA-256 digest. ## Licensing and attribution Original VariantHound code and documentation are Apache-2.0. Benchmark facts and future processed tables retain their upstream sources' terms and attribution requirements, so the aggregate dataset uses `license: other`. See `docs/DATA.md`, the per-case references, and the source manifest before redistribution or publication. OMIA data should cite DOI `10.25910/2AMR-PV70` and acknowledge the Sydney Informatics Hub. OMIA asks users to contact its team about publications that rely on the MySQL dump or extended data. ## Known limitations - Three demonstration cases are not an adequate performance benchmark. - The ontology vocabulary in the demo is intentionally compact and includes internal `VH:*` terms. - Canonical gene symbols are not present in the Compara bulk export and remain null until a separately pinned identifier-enrichment source is applied; stable Ensembl gene IDs are the join keys. - A learned ranking model is not supported by the current sample size. See `DATA_CONTRACT.md` for the package layout and field-level expectations.