| ---
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| pretty_name: VariantHound Research Snapshot
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| language:
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| - en
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| license: other
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| size_categories:
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| - 1M<n<10M
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| tags:
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| - biology
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| - genomics
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| - veterinary
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| - phenotype
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| - tabular
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| configs:
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| - config_name: benchmark_cases
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| data_files:
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| - split: test
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| path: data/benchmark_cases.jsonl
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| ---
|
|
|
| # VariantHound Research Snapshot
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|
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| VariantHound is an explainable, phenotype-aware research system for ranking candidate genes in canine inherited disease. This dataset repository contains the compact, redistributable artifacts generated from the public [VariantHound source repository](https://github.com/TinyAnts/VariantHound).
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|
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| > Research and educational use only. This snapshot is not a diagnostic dataset or medical device, and its rankings require expert review and experimental validation.
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|
|
| ## Current contents
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|
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| The release contains:
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| - three literature-grounded canine benchmark cases;
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| - source and orthology provenance manifests;
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| - a checksum-pinned Ensembl 116 dog-human-mouse orthology snapshot in releases built by the publication workflow;
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| - a checksum pin for HPO 2026-09-01 and its matching human annotations, plus normalized JSONL in publication-workflow releases;
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| - a dated Monarch 2026-09-02 evidence snapshot with a checksum-pinned HGNC stable-ID crosswalk;
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| - a direct, retrieval-dated MGI genotype/phenotype snapshot with reconciled stable gene IDs;
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| - a processed canine OMIA snapshot with phenes, stable-ID gene evidence, causal variants, breeds, and publications;
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| - a compact PHENIO HP/MP/uPheno semantic-similarity closure with upstream ontology versions;
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| - content-addressed browser shards for terms, phenotype closure, stable-ID gene profiles, and orthology;
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| - machine-readable schemas for the published contracts;
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| - evaluation, data, orthology, HPO, Monarch, MGI, OMIA, and PHENIO documentation;
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| - a release manifest containing the source Git commit, byte sizes, and SHA-256 checksums.
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| `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.
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|
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| ## Evaluation safety
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| 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.
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|
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| ## Orthology status
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| 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.
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| ## HPO status
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| 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.
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|
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| ## Monarch status
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| 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.
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|
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| ## Direct MGI status
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| 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.
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| ## OMIA status
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| 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.
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| ## PHENIO status
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| 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.
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|
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| ## Reproducibility
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| 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.
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|
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| ## Licensing and attribution
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| 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.
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| 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.
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| ## Known limitations
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| - Three demonstration cases are not an adequate performance benchmark.
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| - The ontology vocabulary in the demo is intentionally compact and includes internal `VH:*` terms.
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| - 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.
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| - A learned ranking model is not supported by the current sample size.
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| See `DATA_CONTRACT.md` for the package layout and field-level expectations.
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|
