LitCoin MCP Server

MCP server for the LitCoin Knowledge Graph (KG) - query LitCoin knowledge graph for nodes, edges, relationships as well as semantic similarity search over nodes and relationships. It supports semantic + structural LitCoin knowledge graph access for AI agents via MCP.

This MCP server exposes the following tools:

• get_node(node_id: CURIE str)
• Get information about a specific node by CURIE.
• get_node_edges(node_id: CURIE str)
• Get all edges connected to a node.
• get_edges_between(source_id: CURIE str, target_id: CURIE str)
• Find all edges connecting two nodes by CURIEs
• get_semantic_similar_nodes(query: str, top_k: int = 10, k_per_index: int = 2)
• Find top_k semantically similar nodes to an input text query
• get_semantic_similar_edges(query: str, top_k: int = 10, k_per_index: int = 2)
• Find top_k semantically similar relationships to an input text query

Note that for semantic search tools to work, this MCP server assumes Neo4j embedding vector indexes already exist.

Response Format

• All responses are JSON serializable.
• Embedding vectors stored in Neo4j are never returned to the client.
• Semantic search results are sorted by similarity score (descending).

Recommended Usage: Use with uvx

No installation needed! Use uvx to run the server in isolated environments.

Configuration

Environment Variables

The following environmental variables must be configured for this LitCoin MCP Server:

• OPENAI_API_KEY - OPENAI API Key for semantic search related tools

such as get_semantic_similar_nodes and get_semantic_similar_edges. the embedding vectors for nodes and edges in the LitCoin KG were created using the text-embedding-3-small model from OpenAI. It's recommended to use the same model to generate embeddings for input text queries to ensure dimensional compatibility for semantic search related tools.

• NEO4J_USERNAME - LitCoin Neo4j server authentication username.
• NEO4J_PASSWORD - LitCoin Neo4j server authentication password.
• NEO4J_URI - LitCoin Knowledge Graph endpoint (default: bolt://litcoin-graph.apps.renci.org:7687)

MCP CLient (e.g., Goose, Claude Desktop) Configuration

#### Using uvx The easiest way to use this MCP server is with uvx, which runs it in isolated environments without installation:

{
  "mcpServers": {
    "litcoin": {
      "command": "uvx",
      "args": ["litcoin-mcp"]
    }
  }
}

#### For Local Development When running from source, use the full uv command:

{
  "mcpServers": {
    "robokop": {
      "command": "uv",
      "args": [
        "run",
        "--directory",
        "/absolute/path/to/litcoin-mcp",
        "python",
        "run_server.py"
      ]
    }
  }
}

Note: Replace /absolute/path/to/litcoin-mcp with your actual path.