A unified biomedical graph database that integrates 80+ primary data sources (genes, proteins, compounds, diseases, pathways, and clinical data) into a single queryable graph with billions of cross-reference edges. Its native MCP server gives LLMs direct access to structured, authoritative, up-to-date biomedical data.
BRCA1 >> ensembl >> uniprot >> pdb[resolution<2.0]One line, three databases: find BRCA1 in Ensembl, map to UniProt proteins, and return high-resolution PDB structures.
Website: sugi.bio/biobtree. Live MCP endpoint, REST API, examples, and full documentation.
BioBTree exports a biolink-typed KGX knowledge graph. A human-scoped, Neo4j-ready subgraph (~40M nodes / ~132M edges) is published on Zenodo under CC BY-NC-SA 4.0. See docs/kg_export.
Related MCP server: BioMCP
BioBTree v2: Grounding LLM Responses with Large-Scale Structured Biomedical Data
The preprint, detailing the graph architecture and comparative LLM use cases, is on Zenodo: https://zenodo.org/records/18962899
BioBTree v1: F1000Research
Free for everyone. Use it live at sugi.bio, or self-host it under AGPL-3.0.
For commercial or closed-source use, a commercial license is available. Get in touch at tamer.gur07@gmail.com.
This server cannot be deployed
Open Targets MCP — disease/target/drug knowledge graph.
Monarch Initiative MCP — biomedical knowledge graph.
Knowledge graph ingestion, entity search, ontology analysis, and CoPass scoring.
Connect AI clients to biomedical data and tools.
