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SAGE PVPDP-KG (curated v1)
Patient x Variant x Protein x Drug x Pathway knowledge graph used by the SAGE
biomedical agent. Stored as a single SQLite file kg.sqlite.
Schema
| Table | Rows | Source |
|---|---|---|
| variant | 10 | ClinVar / ClinGen curated |
| neoantigen | 5 | TESLA / IEDB curated |
| pgx | 7 | CPIC curated |
| synergy | 5 | NCI-ALMANAC / DrugComb / GDSC2 |
| pathway | 6 | Reactome (Homo sapiens) |
| pathway_member | 33 | Reactome members |
| meta | 3 | build provenance |
Use from Python
from sage.server.world.pvpdp_kg import PVPDPKnowledgeGraph
kg = PVPDPKnowledgeGraph() # auto-downloads kg.sqlite from this repo
print(kg.get_variant("CV:128144"))
KG_CACHE_DIR controls where kg.sqlite lands locally. Set
SAGE_KG_NO_DOWNLOAD=1 to force the curated in-memory fallback.
Build / extend
python data/build_pvpdp_kg.py --out data/cache/kg.sqlite
The build script always inserts the curated records bundled in
sage/server/world/pvpdp_kg.py, and optionally enriches with raw downloads
in ~/.sage/cache/ (ClinVar variant_summary.txt.gz, CPIC, Reactome).
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