ncbi-kg-mcp

# ncbi-kg-mcp MCP server for the [NCBI Knowledge Graph](https://github.com/monideep2255/ncbi_ai_agents) - a BioLink-compliant glucose metabolism graph with 82,517 nodes and 263,404 edges. Query genes, diseases, variants, proteins, pathways, and more from any LLM. ## Install ```bash pip install ncbi-kg-mcp ``` ## Configure Add to your `.mcp.json` (Claude Code, Cursor, Cline, etc.): ```json { "mcpServers": { "ncbi-kg": { "command": "ncbi-kg-mcp" } } } ``` That's it. No API keys, no database credentials, no repo cloning needed. ## Tools (5) | Tool | Input | Description | |------|-------|-------------| | `query` | `question: str` | Ask a natural language question - auto-translated to Cypher | | `cypher` | `query_text: str` | Run a read-only Cypher query directly | | `get_stats` | None | Get node and edge counts by type | | `get_schema` | None | Get graph schema - node types, relationships, patterns | | `get_neighbors` | `node_id: str` | Get 1-hop neighbors of a node (e.g., "NCBIGene:2645") | ## Example Ask your LLM: *"What genes are associated with MODY?"* The LLM calls the `query` tool, which translates to Cypher, executes against Neo4j, and returns a synthesized answer with raw data. ## Graph Data - **8 node types**: Gene, Disease, SequenceVariant, BiologicalProcess, MolecularActivity, Protein, CellularComponent, Pathway - **15 relationship types**: GENE_ASSOCIATED_WITH_CONDITION, IS_SEQUENCE_VARIANT_OF, CAUSES, INVOLVED_IN, ENABLES, and more - **Sources**: NCBI Gene, ClinVar, MedGen, MONDO, GO, UniProt, Reactome ## Configuration | Env Variable | Default | Description | |-------------|---------|-------------| | `NCBI_KG_API_URL` | `https://ncbi-kg-api-production.up.railway.app` | API base URL | Override the API URL to point to a local backend: ```json { "mcpServers": { "ncbi-kg": { "command": "ncbi-kg-mcp", "env": {"NCBI_KG_API_URL": "http://localhost:8001"} } } } ``` ## Links - [Full documentation](https:…