mcp-proto-okn: Natural-language access to open scientific knowledge graphs through the Model Context Protocol
Authors: Peter W. Rose, Benjamin M. Good, Amanda M. Saravia-Butler, Charlotte A. Nelson, James P. Balhoff, Yaphet Kebede, Patricia L. Whetzel, Christopher Bizon, +2 more
Organizations: San Diego Supercomputer Center, University of California San Diego, La Jolla, CA 92093, USA · The Scripps Research Institute, La Jolla, CA 92037, USA · Amentum, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA 94035, USA · Mate Bioservices, Redwood City, CA 94065, USA · Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27517, USA · Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158, USA
MCP Server Proto-OKN (mcp-proto-okn) is a Python-based Model Context Protocol server that enables AI assistants to discover, inspect, query and integrate scientific knowledge graphs through natural language. The server provides graph routing, schema inspection, SPARQL execution, ontology expansion, multi-graph querying, and transcript generation, lowering the barrier to cross-domain knowledge graph analysis for biomedical and scientific users. mcp-proto-okn is implemented in Python using the FastMCP framework and is available at https://github.com/sbl-sdsc/mcp-proto-okn. Documentation, client configuration instructions, and example analysis transcripts are provided in the GitHub repository.