Abstract
Biomedical knowledge is fragmented across siloed databases -- Reactome for pathways, STRING for protein interactions, Gene Ontology for functional annotations, this http URL for study registries, and dozens more. Researchers routinely download flat files from each source and write bespoke scripts to cross-reference them, a process that is slow, error-prone, and not reproducible. We present two open-source biomedical knowledge graphs -- Pathways KG (118,686 nodes, 834,785 edges from 5 sources) and Clinical Trials KG (7,774,446 nodes, 26,973,997 edges from 5 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 Cypher loading, and portable snapshot export. Second, we demonstrate cross-KG federation: loading both snapshots into a single graph tenant enables property-based joins across datasets, answering questions like ``Which biological pathways are disrupted by drugs currently in Phase~3 trials for breast cancer?'' -- a query that neither KG can answer alone. Third, we introduce schema-driven MCP server generation: each KG automatically exposes typed tools for LLM agents via the Model Context Protocol, enabling natural-language access to graph queries without manual tool authoring. All data sources are open-license (CC~BY~4.0, CC0, OBO). Snapshots, ETL code, and MCP configurations are publicly available. The combined federated graph (7.89M nodes, 27.8M edges) loads in 76 seconds on commodity hardware (Mac Mini M4, 16GB RAM), and the signature cross-KG query -- ``which pathways are disrupted by drugs in Phase~3 breast cancer trials?'' -- returns validated results in 2.1 seconds.
Abstract (translated)
URL
https://arxiv.org/abs/2603.15080
