Open Biomedical Knowledge Graphs at Scale: Construction, Federation, and AI Agent Access with Samyama Graph Database

arXiv:2603.15080v3 Announce Type: replace-cross
Abstract: Biomedical knowledge is fragmented across siloed databases — Reactome for pathways, STRING for protein interactions, ClinicalTrials.gov for study registries, DrugBank for drug vocabularies, DGIdb for drug-gene interactions, SIDER for side effects. We present three open-source biomedical knowledge graphs — Pathways KG (118,686 nodes, 834,785 edges from 5 sources), Clinical Trials KG (7,774,446 nodes, 26,973,997 edges from 5 sources), and Drug Interactions KG (32,726 nodes, 191,970 edges from 3 sources) — built on Samyama, a high-performance graph database written in Rust.
Our contributions are threefold. First, we describe a reproducible ETL pattern for constructing large-scale KGs from heterogeneous public data sources, with cross-source deduplication, batch loading (Python Cypher and Rust native loaders), and portable snapshot export. Second, we demonstrate cross-KG federation: loading all three snapshots into a single graph tenant enables property-based joins across datasets. Third, we introduce schema-driven MCP server generation for LLM agent access, evaluated on a new BiomedQA benchmark (40 pharmacology questions): domain-specific MCP tools achieve 98% accuracy vs. 85% for schema-aware text-to-Cypher and 75% for standalone GPT-4o, with zero schema errors.
All data sources are open-license. The combined federated graph (7.9M nodes, 28M edges) loads in approximately 3 minutes on commodity cloud hardware, with single-KG queries completing in 80-100ms and cross-KG federation joins in 1-4s