# Direct MGI ingestion

VariantHound treats Mouse Genome Informatics as the primary source for mouse genotype-to-Mammalian Phenotype evidence. The snapshot uses the official reports retrieved on 2026-09-12 and the MP ontology release declared as `2026-08-25`.

## Pinned inputs

`data/manifests/mgi-2026-09-12.json` pins byte counts, Last-Modified timestamps, and SHA-256 digests for:

- `MGI_GenePheno.rpt` — genotype-to-MP annotations;
- `MGI_Gene_Model_Coord.rpt` — GRCm39 NCBI/Ensembl gene models;
- `MGI_EntrezGene.rpt` — official MGI marker-to-NCBI Gene mappings;
- `MPheno_OBO.ontology` — the MP hierarchy.

MGI exposes these reports at moving URLs rather than dated archive paths. This snapshot is therefore retrieval-dated, checksum-pinned, and marked `current-snapshot-only`; refreshing it is a deliberate new data release.

## Identifier reconciliation

The two official MGI crosswalk reports are compared rather than assigned an arbitrary priority. This release contains ten MGI IDs with conflicting NCBI Gene IDs between the reports; two occur in phenotype evidence and affect 26 rows. Another 1,917 phenotype-bearing marker IDs have no Ensembl or NCBI join ID and affect 6,487 rows.

All such data is retained for audit, with `id_status` or `mapping_status` set to `conflict` or `unresolved`, but `rank_eligible` is false. No symbol-only join is attempted. The remaining 276,606 genotype-phenotype rows are rank-eligible.

## Materialization

```bash
npm run ingest:mgi -- --download
```

The command produces:

| File | Contents |
|---|---|
| `mp_terms.jsonl` | MP IDs, labels, hierarchy, alternate IDs, and obsolescence |
| `gene_crosswalk.jsonl` | Every phenotype-bearing MGI marker and its reconciled stable IDs/status |
| `genotype_phenotypes.jsonl` | Genotype, allele, background, publication, MP, and mapping status |
| `snapshot.json` | Source provenance, safety policies, exact counts, and output checksums |

Each evidence row has a deterministic `MGI-EVIDENCE:<sha256>` ID derived from all eight source columns. These IDs and genotype/disease groupings are available to the masking layer before feature construction.

## Monarch overlap

The Monarch mouse association export is a downstream integrated view of MGI. Direct MGI and Monarch records must be provenance-linked and deduplicated before scoring; they are not independent supporting observations. Direct MGI provides the richer genotype, allele, background, and publication context and is the preferred primary evidence record.