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neuralninja110/sage-pvpdp-kg

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… See the full description on the dataset page: https://huggingface.co/datasets/neuralninja110/sage-pvpdp-kg.

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Dataset Card

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

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).