MCP interface

MCP interface (TogoMCP)

TogoMCP is a Model Context Protocol (MCP) server developed by DBCLS that provides LLM-based AI agents with seamless access to a wide range of life sciences databases hosted on RDF Portal.

Through TogoMCP, users of AI systems such as Claude, ChatGPT, and Gemini can more easily search, explore, and integrate complex biological data using natural language, without requiring knowledge of SPARQL or database-specific schemas.

MCP Server Endpoint: https://togomcp.rdfportal.org/mcp

Key features

  • Multi-database access — Query proteins, genes, chemicals, diseases, pathways, and more across 20+ integrated databases including UniProt, PubChem, ChEMBL, PDB, Reactome, ClinVar, and others, all through a single MCP endpoint.
  • SPARQL & RDF-based — Built on Semantic Web technologies. TogoMCP facilitates query generation for the RDF Portal’s SPARQL endpoint, enabling the retrieval of accurate, structured data that leverages rich cross-references across datasets.
  • ID conversion — Powered by TogoID, the server converts identifiers across 65+ biological databases, including cross-category conversions (e.g., disease IDs to gene IDs) with semantic relationship annotations.
  • AI-ready — It is designed for use by AI agents. It can be used with any AI model that can access remote MCP servers, including Claude Desktop, ChatGPT, and Gemini CLI.

Available tools

TogoMCP exposes a rich set of tools organized into the following categories:

  • Database & information — List available databases, retrieve metadata schemas (ShEx), SPARQL examples, and named graphs.
  • Keyword search — Search across UniProt, ChEMBL (molecules and targets), PDB, Reactome, Rhea, and MeSH using keywords.
  • SPARQL query — Execute custom SPARQL queries on any RDF database in the portal.
  • ID conversion (TogoID) — Convert and look up identifiers across databases, discover available conversion routes.
  • NCBI E-utilities — Search, summarize, and fetch records from NCBI databases (Gene, Taxonomy, ClinVar, MedGen, PubMed, PubChem).
  • PubChem-specific — Look up compound IDs and retrieve detailed molecular descriptors.

Getting started

TogoMCP can be connected to AI assistants in just a few steps. Setup guides are available for Claude Desktop, ChatGPT, and Gemini CLI.

For detailed setup instructions, usage examples, the complete list of available databases and tools, and information about complementary MCP servers, please visit the TogoMCP website.

The source code is open and available on GitHub: dbcls/togomcp.