Monarch Knowledge Graph ingestion
VariantHound uses the dated Monarch KG 2026-09-02 release for two compact, provenance-rich association views:
- human gene-to-disease associations;
- mouse gene-to-Mammalian Phenotype associations.
The latter is an integrated view whose primary source is MGI. It is retained for comparison and provenance, but it must not be scored as an independent evidence track alongside the same underlying direct MGI record.
Stable human identifiers
Monarch represents human genes with HGNC IDs. data/manifests/monarch-kg-2026-09-02.json therefore also pins the official HGNC complete-set export retrieved on 2026-09-12. The transform resolves each HGNC ID to NCBI Gene and Ensembl gene IDs before publication. Symbols are checked for disagreement but remain display fields, never join keys.
Of 4,800 human genes in this release, 4,799 have both NCBI Gene and Ensembl IDs; one has an NCBI Gene ID but no Ensembl ID. No human association is accepted without at least one stable cross-database join ID.
Materialization
npm run ingest:monarch -- --download
The command verifies four pinned inputs and writes:
| File | Contents |
|---|---|
human_gene_disease.jsonl |
Deduplicated HGNC/NCBI/Ensembl-to-MONDO associations |
mouse_gene_phenotype.jsonl |
MGI gene-to-MP associations with publications and source attribution |
snapshot.json |
Release metadata, exact counts, policies, and output checksums |
Each record receives a deterministic MONARCHKG:<sha256> evidence ID derived from the complete source row. The human export contains 218 exact duplicate rows; they collapse to one evidence record per stable hash. No non-exact evidence is merged.
Leakage and source overlap
The output is marked current-snapshot-only. Historical evaluation requires a dated Monarch release that predates the held-out case. Evidence masking operates on deterministic evidence IDs and disease IDs before feature construction.
Monarch is an aggregator. primary_source and aggregator_sources are preserved on every row. Records whose primary source is infores:mgi must be provenance-linked to the direct MGI snapshot and deduplicated rather than counted as corroboration.