# 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.gz` dump retrieved on 2026-09-12; and
- the matching `omia_gene_export.csv` mapping 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:

```bash
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.