| # PHENIO / uPheno ingestion | |
| VariantHound uses PHENIO as the cross-species phenotype backbone for deterministic semantic similarity. PHENIO is an application ontology that includes uPheno and multiple species phenotype ontologies; VariantHound does not copy the complete integrated graph into its public dataset. | |
| ## Pinned inputs | |
| `data/manifests/phenio-2026-09-01.json` pins PHENIO release `v2026-09-01` by tag, source commit, immutable GitHub asset IDs, byte counts, and SHA-256 digests. The transform consumes: | |
| - `phenio-relation-graph.gz`, the release's materialized relation graph; and | |
| - `phenio-upstream-versions.tsv`, which records the integrated ontology versions. | |
| The relation graph was generated upstream with equivalence-as-subclass, subclass output, and reflexive subclass relations. VariantHound preserves that meaning as an `entailed-reflexive-subclass-closure` rather than treating the rows as asserted direct edges. | |
| ## Compact output | |
| `pipelines/ingest_phenio.py` scans all 82,128,289 relations but retains only the 3,972,487 subclass-closure rows needed for human/mouse cross-species comparison: | |
| | Subject | Retained ancestors | | |
| |---|---| | |
| | `HP` | `HP`, `UPHENO` | | |
| | `MP` | `MP`, `UPHENO` | | |
| | `UPHENO` | `UPHENO` | | |
| The output `phenotype_closure.tsv.gz` contains `phenotype_id` and `ancestor_id`. It includes one reflexive row for each retained phenotype, enabling exact self-matches. `upstream_versions.tsv` keeps the release-level provenance for all integrated sources. Labels and asserted local hierarchies remain in the separately pinned HPO and MGI snapshots. | |
| Relations to anatomy, qualities, diseases, genes, and phenotype ontologies not used by VariantHound's first ranking path are excluded. This keeps the processed package compact without replacing PHENIO's inferred cross-species bridge with a hand-authored mapping. | |
| ## Evaluation scope | |
| This is a current release backbone, not a historical snapshot. It may be used for current retrieval and discovery simulation when case-specific evidence is masked before feature construction, but it cannot support temporal evaluation of older cases. | |
| ## Reproduction | |
| Place the two pinned assets in `dist/phenio/raw/`, then run: | |
| ```bash | |
| python3 pipelines/ingest_phenio.py | |
| ``` | |
| Use `--download` to fetch the immutable release assets. Every source checksum, relation count, prefix-pair count, reflexive-term count, and output checksum is verified before the snapshot is accepted. | |