| # Human Phenotype Ontology ingestion | |
| VariantHound uses HPO as the human phenotype hierarchy and as the source of human disease and gene phenotype annotations. The production snapshot is pinned to ontology release `v2026-09-01`; `phenotype.hpoa` declares annotation version `2026-09-02`. | |
| ## Pinned assets | |
| `data/manifests/hpo-2026-09-01.json` records the immutable GitHub release asset ID, byte count, and SHA-256 for: | |
| - `hp.obo` — ontology terms, synonyms, alternate IDs, obsolescence, replacements, and `is_a` edges; | |
| - `genes_to_phenotype.txt` — NCBI Gene-to-HPO associations with disease and frequency context; | |
| - `phenotype.hpoa` — disease-to-HPO annotations, including evidence, references, frequencies, and negation. | |
| Downloads use the GitHub asset API URL (`/releases/assets/{asset_id}`) with `Accept: application/octet-stream`. The public filename URL is retained for provenance, but is not used for reproducible retrieval: GitHub release assets are replaceable and the filename URL can therefore return bytes that do not match the release asset record. | |
| ## Materialization | |
| ```bash | |
| npm run ingest:hpo -- --download | |
| ``` | |
| The command verifies every raw artifact before parsing and writes four deterministic files under `dist/hpo/materialized/`: | |
| | File | Contents | | |
| |---|---| | |
| | `ontology_terms.jsonl` | One ontology term per line, sorted by HPO ID | | |
| | `gene_phenotypes.jsonl` | Human gene-phenotype rows with NCBI Gene IDs | | |
| | `disease_annotations.jsonl` | Disease-phenotype rows with explicit `negated` state | | |
| | `snapshot.json` | Release metadata, exact counts, output byte sizes, and SHA-256 digests | | |
| The ingest fails on checksum drift, unexpected headers, invalid stable IDs, unresolved HPO identifiers, annotation-version drift, or any exact-count change. Empty values and the HPO `-` sentinel become JSON `null`; source identifiers, evidence codes, frequencies, references, and curation strings are otherwise preserved. | |
| ## Leakage boundary | |
| This release is a current snapshot and is marked `current-snapshot-only`. It may be used for the normal current-data ranking mode, but it must not be used to claim historical or temporal discovery performance. A temporal benchmark requires a separately pinned HPO and annotation snapshot whose release predates the held-out case. Direct disease and evidence masks are applied after source ingestion and before feature construction. | |
| ## Scope | |
| This module normalizes the HPO layer only. It does not infer dog-to-human mappings, merge genes by symbol, or combine Monarch, MGI, or OMIA evidence. Those sources have independent pins and ingestors so their provenance and failure modes remain separable. | |