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
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.