MCP Proto-OKN Server

A single Model Context Protocol (MCP) server that exposes 30+ Proto-OKN knowledge graphs through one unified interface. The server enables AI assistants (Claude, ChatGPT, GitHub Copilot, etc.) to discover graphs, inspect their schemas, query them with SPARQL, bridge identifiers across graphs, and combine results from multiple sources — all through natural-language conversation. The graphs are hosted on the Open Knowledge Network (OKN) federation platform and cataloged in the OKN Knowledge Graph Registry.

Beta: the proto-okn MCP server is in beta. We welcome feedback and bug reports via issues.

Cross-Graph Demo: SPOKE, ProKN, BioBricks, SAWGraph

Video · Presentation

Note: MCP URL and installation instructions have changed. Updated instructions

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Features

• 🌐 Unified access — one MCP server, 30+ knowledge graphs, one endpoint
• 🔎 Graph discovery — list and filter graphs by domain or entity type, or rank them by keyword overlap with a question (a lexical prefilter over registry metadata; the assistant makes the final selection)
• 📐 Schema inspection — understand each graph’s classes, predicates, and properties before writing queries
• 🧭 Per-graph SPARQL — query any individual graph with automatic FROM-clause injection
• 🔗 Cross-graph bridging — built-in identifier maps (Ensembl ↔ NCBI Gene ↔ Symbol; CAS, DTXSID, InChIKey; MONDO, FIPS, NAICS, …)
• 🧬 Multi-graph queries — run different SPARQL across multiple graphs in a single call and merge results
• 🌳 Ontology-driven search expansion — queries are automatically expanded using ontology hierarchies (MONDO, UBERON, HP, GO, CL, ChEBI, …) via Ubergraph, so a query for “arthritic joint disease” matches all of its subtypes without manual enumeration
• 🖼️ Schema visualization & transcripts — generate Mermaid class diagrams and chat transcripts directly from the conversation

Architecture

Workflow Example