DATA_CONTRACT.md

VariantHound Hugging Face data contract

Package layout

Path	Purpose
data/benchmark_cases.jsonl	One validated canine benchmark case per line, sorted by case ID
data/source_manifest.json	Upstream source access, pinning, redistribution, and attribution policy
data/ensembl-compara-116.json	Immutable Ensembl 116 artifact checksums, assemblies, and expected row counts
data/hpo-2026-09-01.json	Immutable HPO asset IDs, checksums, and expected normalized counts
data/monarch-kg-2026-09-02.json	Dated Monarch/HGNC artifacts and exact normalized counts
data/mgi-2026-09-12.json	Retrieval-dated MGI/MP artifacts, conflict policy, and exact counts
data/omia-2026-09-12.json	Retrieval-dated OMIA dump and official gene-crosswalk checksums
data/phenio-2026-09-01.json	Immutable PHENIO relation-graph assets and exact compact-closure counts
data/orthology_manifest.json	Release-qualified dog-human-mouse mapping policy or pinned mapping snapshot
data/hpo/snapshot.json	HPO release metadata and normalized-file integrity records in full releases
data/hpo/ontology_terms.jsonl	HPO term hierarchy, synonyms, alternate IDs, and obsolescence
data/hpo/gene_phenotypes.jsonl	NCBI Gene-to-HPO annotations with disease and frequency context
data/hpo/disease_annotations.jsonl	Disease-to-HPO annotations with references, evidence, and negation
data/monarch/snapshot.json	Monarch release, deduplication, provenance, and output integrity records
data/monarch/human_gene_disease.jsonl	Stable-ID human gene-to-MONDO evidence
data/monarch/mouse_gene_phenotype.jsonl	MGI gene-to-MP evidence with primary-source attribution
data/mgi/snapshot.json	Direct MGI provenance, identifier policies, and output integrity records
data/mgi/mp_terms.jsonl	Mammalian Phenotype hierarchy and identifier status
data/mgi/gene_crosswalk.jsonl	Phenotype-bearing MGI markers with reconciled NCBI/Ensembl IDs
data/mgi/genotype_phenotypes.jsonl	Direct genotype-to-MP evidence and rank-eligibility state
data/omia/snapshot.json	Canine OMIA provenance, masking and output-integrity contract
data/omia/genes.jsonl	OMIA internal-to-NCBI Gene resolution for canine genes
data/omia/phenes.jsonl	Canine phenes, clinical text, inheritance, breeds and ontology links
data/omia/gene_phene_evidence.jsonl	Stable-ID canine gene–phene evidence with discovery mask IDs
data/omia/causal_variants.jsonl	Variants linked to canine single-locus traits with assemblies and publications
data/omia/publications.jsonl	Publications referenced by canine OMIA phenes or variants
data/phenio/snapshot.json	PHENIO release, closure semantics, prefix policy, and output integrity
data/phenio/phenotype_closure.tsv.gz	Entailed reflexive HP/MP/uPheno subclass closure used for semantic similarity
data/phenio/upstream_versions.tsv	Versions of all ontologies integrated into the pinned PHENIO release
data/browser/manifest.json	Content-addressed browser collection map, source fingerprints, counts, and limitations
data/browser/{collection}/*	Sixteen deterministic gzip buckets per terms, closure, gene-profile, and orthology collection
data/ml-readiness-policy.json	Versioned independent-sample and learned-model promotion thresholds
schemas/*.schema.json	Machine-readable contracts used by the source repository
docs/*.md	Data provenance, leakage-safe evaluation, source-ingestion, and ranking guidance
release-manifest.json	Dataset version, source commit, file sizes, and SHA-256 digests

The release builder uses an explicit source-to-destination allowlist. Files under data/raw, data/processed, browser build directories, credentials, VCF/BCF files, and complete third-party database exports are never copied implicitly. The complete OMIA SQL dump is excluded; only its verified canine transform can be selected.

Benchmark case fields

Each line in data/benchmark_cases.jsonl contains:

• id, label, species, breed, and expected_gene;
• disease_group_id, the indivisible split and resampling unit;
• phenotypes.present and phenotypes.excluded ontology identifiers;
• publication_year;
• evaluation.discovery_mask_evidence_ids and evaluation.discovery_mask_disease_ids;
• evaluation.temporal_status and an exclusion reason when applicable;
• a literature reference with label and URL.

Cases are benchmark inputs, not independent training rows. Disease-level grouping and temporal availability must be preserved in any downstream evaluation.

Release integrity

release-manifest.json is valid only when:

1. every listed payload path exists and no unlisted file is present;
2. every byte count and lowercase SHA-256 digest matches;
3. the dataset version and source Git commit are recorded;
4. the package was built after the repository data validator passed.

The upload script rechecks all four conditions before contacting Hugging Face.