Canine OMIA ingestion
VariantHound uses a retrieval-dated, checksum-pinned subset of the Online Mendelian Inheritance in Animals (OMIA) database. The transform reads the official MySQL dump as data without executing SQL and joins it to OMIA's separate internal-to-NCBI Gene export.
Pinned inputs
data/manifests/omia-2026-09-12.json records the byte count and SHA-256 digest of:
- the complete
omia.sql.gzdump retrieved on 2026-09-12; and - the matching
omia_gene_export.csvmapping OMIA internal gene IDs to NCBI Gene IDs.
The raw database dump is never committed or redistributed. Only the canine (NCBI Taxonomy 9615) normalized products are eligible for the processed Hugging Face package. OMIA requests citation of DOI 10.25910/2AMR-PV70, an acknowledgement of the Sydney Informatics Hub, and contact about publications relying on the MySQL dump or extended OMIA data.
Stable identity and ranking eligibility
OMIA's gene_id is an internal identifier and is not assumed to equal NCBI Gene. pipelines/ingest_omia.py resolves it only through the pinned official gene export. Symbols remain display-only. Missing mappings are retained with mapping_status: unresolved and rank_eligible: false.
The normalized files are:
| File | Contents |
|---|---|
genes.jsonl |
Canine OMIA genes and their official NCBI Gene resolution status |
phenes.jsonl |
Canine phenes, OMIA record IDs, inheritance, clinical text, breeds, and ontology links |
gene_phene_evidence.jsonl |
Stable-ID gene–phene evidence with deterministic masking identifiers |
causal_variants.jsonl |
Variants linked to canine single-locus traits, with genes, breeds, publications, HGVS fields, and stated reference assembly |
publications.jsonl |
Publications referenced by canine phenes or causal variants |
Leakage and temporal policy
Each gene–phene and causal-variant row has a deterministic evidence_id and mask_ids containing both the evidence identifier and the binomial OMIA record identifier. Case-specific discovery evidence must be masked before feature construction, aggregation, or candidate scoring.
The upstream dump is moving and has no historical release tag. This snapshot is therefore current-snapshot-only and cannot support temporal evaluation. A publication year is not evidence that the complete OMIA record, gene assignment, or current curation state existed in that year.
Coordinates
OMIA's variant reference_sequence is preserved verbatim. Recognized assembly names are copied into assembly; other references remain source-reference-only. Coordinates from different canine assemblies are never combined or lifted silently.
Reproduction
Place the two pinned inputs in dist/omia/raw/, then run:
python3 pipelines/ingest_omia.py
Use --download to retrieve both artifacts from the official URLs. Every input checksum and every exact normalized row count must match the release descriptor or the transform stops.